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Human Gene Nomenclature 

Human Gene Nomenclature

Chapter:
Nomenclature
Author(s):

Harriet S. Meyer

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Human Gene Nomenclature

The International System for Human Gene Nomenclature (ISGN) was inaugurated in 19791,2 and has been continually updated. The Human Gene Mapping Nomenclature Committee, which developed the ISGN, put forth a “one human genome–one gene language” principle:

Certainly there exists a genetic and molecular basis for a single human gene language without dialects. All human nuclear genes as we know them follow the same genetic, molecular, and evolutionary principles…. Thus it is reasonable and logical to develop a standard and consolidated gene nomenclature system rather than have a human gene language based on different gene systems.3(p12)

The committee, known as the HUGO Gene Nomenclature Committee (HGNC), is 1 of 7 committees of the Human Genome Organisation (HUGO) and is “responsible for gene name validation.”4(p115) Gene names and symbols are assigned by the HGNC.5 The human genome is estimated to have approximately 30 000 genes, more than 20 000 of which are represented by active symbols,6 with the remainder to be named in a consistent fashion as genes are discovered.

  • Gene Symbols: A gene symbol is a short term, typically 3 to 7 characters long, that conveys in abbreviated form the name or other attribute of a gene. Human gene symbols usually consist of uppercase letters and may also contain (but never begin with) numerals. Approved gene symbols do not contain Greek letters, roman numerals, superscripts, or subscripts and usually contain no punctuation. In JAMA and the Archives Journals, gene symbols are italicized, per official recommendations.7 Italicizing is a useful way to make clear that a gene, and not a similarly named entity such as a condition or product of the gene, is being discussed. Italics are not necessary in published catalogs of gene symbols.7 For style rules for gene symbols, see Table 3.

Table 3. Style Rules for Gene Symbols (Examples)

Gene Description

Approved

Gene Symbol Rule Illustrated

α-fetoprotein

AFP

Greek letter changed to Latin letter (but not moved to end of symbol: exception to recommendation)

β2-microglobulin

B2M

Greek letter changed to Latin letter; no subscripts or punctuation

α-galactosidase

GLA

Greek letter changed to Latin letter and moved to end of symbol

coagulation factor VIII

F8

roman numeral changed to arabic numeral

β1-galactosidase

GLB1

Greek letter changed to Latin letter and moved with numeral to end of term; no subscripts or punctuation

heterogeneous nuclear ribonucleoprotein A2/B1

HNRPA2B1

no punctuation marks or spaces

MCF.2 cell line–derived transforming sequence

MCF2

no punctuation marks

5′-nucleotidase, cytosolic

NT5C

number moved from the start of symbol; no punctuation

5S RNA, cluster 1

RN5S1@

first character is letter, not number

thromboxane A2 receptor

TBXA2R

no superscripts or subscripts

Approved symbols may represent other entities, such as chromosomal regions, certain syndromes, genes whose existence is inferred (supported by linkage analysis or association with known markers), cloned DNA segments, pseudogenes, and DNA fragments.

Within larger terms, only the gene symbol is italicized:

ADRB246G>A (not: ADRB2 46G>A)

ADRB2 Gly16Arg (not: ADRB2 Gly16Arg)

(For an explanation of 46G>A and Gly16Arg, see “Sequence Variations, Nucleotides,” and “Sequence Variations, Amino Acids,” in 15.6.1, Nucleic Acids and Amino Acids.)

Authors are encouraged to use the most up-to-date gene symbol, which may be verified at the HGNC website in the Human Gene Nomenclature Database (Searchgenes feature),6,8,9 or Entrez Gene.10 The records available in Searchgenes contain “23 fields, with 14 links to other resources,” such as Online Mendelian Inheritance in Man (OMIM, see later in this section), LocusLink, and Swiss-Prot (see 15.6.1, Nucleic Acids and Amino Acids).9 Consistent use of the approved gene symbol provides advantages when searching for information in multiple databases.11

  • Gene Names: Genes are usually named for the molecular product of the gene, the function of the gene, or the condition associated with the gene if known. Gene names are not italicized. As shown directly below, the approved gene names, available in the above mentioned databases, expand Greek letters and do not use subscripts, etc (so that, for instance, in using Searchgenes to find a gene name with a, one would type in “alpha”). Descriptions based on the approved gene names but styled according to the journal in question (eg, using Greek letters and subscripts) or omitting some terms from the full name are permissible in general medical journals.

    approved gene name: the alpha-fetoprotein gene

    description: the α-fetoprotein gene

    approved gene name: the gene for beta-2-microglobulin

    description: the gene for β2-microglobulin

A number of conventions are followed when gene symbols and names are officially designated. Related genes are often assigned symbols by sequentially numbering a stem, the root symbol for the gene family:

  • ABC: root symbol

  • genes: ABCA1, ABCG4, etc

  • TNF: root symbol

  • genes: TNF, TNFAIP1, TNFAIP2, TNFAIP3, etc

Other conventions involve stereotypic abbreviations, eg, CR will often signify a “chromosome region.” (However, a given letter or letter combination does not always signify a conventional usage. For instance, L at or near the end of a symbol often, but not always, indicates “like.”) In Table 4, the conventions in column 3 reflect HGNC recommendations.7 (Note: DNA sequences are available from the Genome Database, http://www.genenames.org/.7)

Table 4. Conventions for Gene Names and Gene Symbols (Examples)

Gene Description

Gene Symbol

Convention Illustrated

Angelman syndrome chromosome region

ANCR

CR: chromosome region

BRCA1-associated protein

BRAP

AP: associated protein

bromodomain containing 1

BRD1

D: domain-containing

chromosome 11 open reading frame 10

C11orf10

orf: lowercase exception for “open reading frame”

calcium modulating ligand

CAMLG

LG: ligand

caspase 1, 2, 3, etc, apoptosis-related cysteine protease

CASP1, CASP2, CASP3, etc

stem (CASP), sequentially numbered

cyclin-dependent kinase inhibitor 1 B

CDKN1B

N: inhibitor

Cornelia de Lange syndrome 1

CDL1

named for condition; L at end in this case does not signify “like”

carpal tunnel syndrome 1

CTS1

named for syndrome

cystic fibrosis transmembrane conductance regulator

CFTR

formerly CF; name modified after discovery of gene product

collagen (type VI, α1), overlapping transcript 1

COLOT1

OT: overlapping transcript

DNA segment sequence

D19S1177E

D: DNA; 19: chromosome 19; S: (unique DNA) segment; E expressed

Down syndrome chromosome region

DCR

CR: chromosome region

deafness, autosomal dominant 4

DFNA4

named for condition

DNA segment sequence

DXS522E

as above; X: X chromosome

DNA segment sequence

DXYS155E

as above; XY: sequence present at homologous sites on chromosomes X and Y

family with sequence similarity 7, member A1

FAM7A1

FAM: family with sequence similarity

fragile site, aphidicolin type, common, fra(10)(q11.2) (see also 15.6.4, Human Chromosomes)

FRA10G

FRA: fragile site; 10: chromosome 10; G: series letter

fragile site, folic acid type, rare, fra(X)(q28)

FRAXF

X: X chromosome; final F: series letter

glucose 6-phosphatase, catalytic (glycogen storage disease type I, von Gierke disease)

G6PC

C: catalytic

glucose-6-phosphate dehydrogenase

G6PD

named for gene product

glucose-6-phosphate dehydrogenase–like

G6PDL

L: “like” sequence

hemoglobin, α1

HBA1

named for gene product

hemoglobin, α1 pseudogene

HBAP1

P: “pseudogene” (compare term directly above)

hair color 1 (brown)

HCL1

named for characteristic

human immunodeficiency virus 1 enhancer binding protein 2

HIVEP2

P: does not always signify “pseudogene”

major histocompatibility complex, class I, A

HLA-A

punctuation exception for HLA genes

homeobox A7

HOXA7

HOX signifies “homeobox” gene family

insulinlike growth factor 2, antisense

IGF2AS

AS: antisense

insulin-dependent diabetes mellitus 10

IDDM10

a type 1 diabetes susceptibility locus, number 10

interleukin 18 binding protein

IL18BP

BP: binding protein

insulin

INS

named for gene product

insulin receptor

INSR

R: receptor

insulin receptor–like

INSRL

R: receptor L: like

loss of heterozygosity 3, chromosomal region 2, gene A

LOH3CR2A

LOH: loss of heterozygosity

melanoma antigen, family A, 2

MAGEA2

named for condition and gene product

mitochondrial ribosomal protein 63

MRP63

M: mitochondrial RP: ribosomal protein

7S mitochondrial DNA

MT7SDNA

MT: mitochondrial

mitochondrially encoded 12S RNA

MT-RNR1

MT: mitochondrial, used with hyphen (punctuation exception)

programmed cell death 1

PDCD1

named for function

pepsinogen A gene cluster

PGA@

@: gene family or cluster

renin

REN

named for gene product

renin binding protein

RENBP

named for gene product; BP: binding protein

5S RNA, cluster 1

RN5S1@

@: gene family or cluster; RN: RNA

schwannomin interacting protein 1

SCHIP1

IP: interacting protein

T-cell, immune regulator 1

TCIRG1

RG: regulator

α2-tubulin

TUBA2

named for gene product

zinc finger protein 160

ZNF160

initial ZNF indicates zinc finger protein

When a gene name or symbol has been changed, both the new and former names (previous symbols) are available in gene databases.6,10 Authors should use the most up-to-date term. The previous symbol may be included parenthetically at first mention:

CYP2A6 (formerly CYP2A3)

SOD1 (formerly ALS and ALS1)

Writing About Genes and Italicizing Gene Symbols.

Observing the rule of italicizing gene symbols makes clear whether the writer is referring to a gene or to another entity that might be confused with a gene.

In any discussion of a gene, it is recommended that the approved gene symbol be mentioned at some point, preferably in the title and abstract if relevant. However, the gene symbol need not be mentioned every time the writer refers to the gene. Authors may refer to genes (or gene loci) by their official gene names or other descriptive expression. Any of these is acceptable, depending on context and syntax. Of names, descriptions, and symbols, only the gene symbol is italicized. Examples are shown below:

Acceptable Expression

Gene Description

Gene Symbol

the breast and ovarian cancer susceptibility gene

breast cancer 1, early-onset gene

BRCA1

the cystic fibrosis locus

cystic fibrosis transmembrane conductance regulator gene

CFTR

the factor VIII locus

coagulation factor VIII, procoagulant component (hemophilia A) gene

F8

the hemophilia A locus

coagulation factor VIII, procoagulant component (hemophilia A) gene

F8

the gene for synapsin I

synapsin I gene

SYN1

the p53 gene

tumor protein p53 (Li-Fraumeni syndrome) gene

TP53

In the foregoing examples, the gene names and descriptions are readily distinguishable from the gene symbols. Sometimes, however, the gene symbol may be easily confused with the abbreviation for the product or condition associated with the gene unless the gene symbol is italicized; for instance:

Gene

Potentially Confusing Nongene Term

ABO

ABO blood group system (see also 15.1, Blood Groups, Platelet Antigens, and Granulocyte Antigens)

APOE

apoE (apolipoprotein E)

EPO

erythropoietin (Epo)

GRIFIN

GRIFIN protein (galectin-related interfiber protein)

HLA-A, HLA-B, etc

HLA-A, HLA-B, etc (see also 15.8.5, Immunology, HLA/Major Histocompatibility Complex)

MS

multiple sclerosis (MS)

many hormone genes, eg, CRH, GHRH, GNRHR, PTH, TRH

hormone name abbreviations, eg, CRH, GHRH, GNRH receptor, PTH, TRH

In some expressions, italics may be moot, for instance, if a gene is named for an enzyme it produces:

Term

Meaning

TH gene

gene for tyrosine hydroxylase

TH gene

gene for tyrosine hydroxylase

In other expressions, italics distinguish different meanings:

Term

Meaning

HD

gene for huntingtin (protein), Huntington disease gene

HD

Huntington disease

person with HD

person with the HD gene, whether the disease-causing or normal form

person with HD

person with Huntington disease

prevalence of HD

prevalence of the HD gene

prevalence of HD

prevalence of Huntington disease; not necessarily equal to prevalence of the HD gene

TH deficiency

impaired functioning of the TH gene

TH deficiency

deficiency of the enzyme TH

Therefore, it is best to make clear by italicizing gene symbols and through context whether the gene or another entity is being discussed.

Gene symbols do not immediately follow the term in the gene name that they might seem to abbreviate, but rather, should relate to the word gene, usually following it:

the guanylate cyclase 2D gene, GUCY2D

Not: the guanylate cyclase 2D (GUCY2D) gene

the Huntington disease gene, HD

the tyrosine hydroxylase gene, TH

The cystic fibrosis transmembrane conductance regulator gene, CFTR, is implicated in cystic fibrosis.

In the following examples, both gene aliases and approved symbols are used (see also 14.11, Abbreviations, Clinical, Technical, and Other Common Terms):

the retinal guanylate cyclase 2D (GUCY2D) gene, GUCY2D

the retinal guanylate cyclase 2D (RetGC1) gene, GUCY2D

Not: the guanylate cyclase 2D (GUCY2D) gene

 

the Huntington disease (HD) gene, HD

the tyrosine hydroxylase (TH) gene, TH

 

The cystic fibrosis (CF) transmembrane conductance regulator gene, CFTR, is implicated in CF.

In discussions of mutations, the gene symbol remains italicized; specific mutations, however, are not italicized (see “Sequence Variations, Nucleotides,” and “Sequence Variations, Amino Acids” in 15.6.1, Nucleic Acids and Amino Acids):

ADRB2 46G>A

mutation of the GUCY2D gene

mutation of GUCY2D

GUCY2D mutation

mutated GUCY2D gene

Objective: To describe the phenotype in 4 families with dominantly inherited cone-rod dystrophy, 1 with an R838C mutation and 1 with an R838H mutation in the guanylate cyclase 2D gene (GUCY2D) encoding retinal guanylate cyclase-1.

LRP5v171: valine substitution at codon 171 of the LRP5 gene

In gene mapping, when the order of genes along the chromosome is known, the genes are listed from short-arm end (pter) to the centromere (cen) or long-arm end (qter) (see 15.6.4, Human Chromosomes):

pter-ENO1-PGM1-AMY1-cen

When the order of genes along the chromosome is not known, the genes are listed alphabetically and parentheses are used:

pter-PGD-AK2-(ACTA,APOA2,REN)-qter

Table 5 presents gene names and symbols from fields covered elsewhere in this chapter.

Table 5. Gene Names and Symbols From Fields Covered Elsewhere in This Chapter

Gene Symbol

Gene Description

15.1, Blood Groups, Platelet Antigens, and Granulocyte Antigens

A4GALT

α-1,4-galactosyltransferase (P blood group)

ABO

ABO blood group (transferase A, α-1-3-N-acetylgalactosaminyltransferase; transferase B, α-1-3-galactosyltransferase)

ACHE

acetylcholinesterase (Yt blood group)

AQP1 (was CO)

aquaporin 1

ART4 (was DO)

ADP ribosyltransferase 4 (Dombrock blood group)

BCAM (was LU)

basic cell adhesion molecule (Lutheran blood group)

BSG

basigin (OK blood group)

C4A

complement component 4A

C4B

complement component 4B

CD44

CD44 antigen (homing function and Indian blood group system)

CD151 (was MER2)

antigen identified by monoclonal antibodies 1D12, 2F7

CR1

complement component (3b/4b) receptor 1, including Knops blood group system

CD55 (was DAF)

CD55, decay accelerating factor (DAF) for complement (Cromer blood group system)

DARC (was FY)

chemokine receptor (Duffy blood group)

ERMAP (was SC)

erythroblast membrane–associated protein (Scianna blood group)

FUT1

fucosyltransferase 1

FUT3

fucosyltransferase 3

GYPA

glycophorin A (includes MN blood group)

GYPB

glycophorin B (includes Ss blood group)

GYPC

glycophorin C (Gerbich blood group)

GYPE

glycophorin E

ICAM4

intercellular adhesion molecule 4, Landsteiner-Wiener blood group

KEL

Kell blood group

P1

P blood group (P1 antigen)

RHCE

Rh blood group, CcEe antigens

RHD

Rh blood group, D antigen

SLC4A1

solute carrier family 4, anion exchanger, member 1 (erythrocyte membrane protein band 3, Diego blood group)

SLC14A1

solute carrier family 14 (urea transporter), member 1 (Kidd blood group)

XG

Xg blood group (pseudoautosomal boundary-divided on the X chromosome)

XK

Kell blood group precursor (McLeod phenotype)

15.2, Cancer (See Also 15.6.3, Oncogenes and Tumor Suppressor Genes)

ACTN1

α1-actinin

ACTN2

α1-actinin

BCL2

B-cell/CLL lymphoma 2

BCL7A

B-cell/CLL lymphoma 7A

CCND1 (formerly BCL1)

cyclin D1

CDC2

cell division cycle 2, G1 to S and G2 to M

CDK2

cyclin-dependent kinase 2

CDKN1A

cyclin-dependent kinase inhibitor 1A (p21, Cip1)

CTNNB1

β1-catenin

MEN1

multiple endocrine neoplasia 1

RB1

retinoblastoma 1 (including osteosarcoma)

RET (formerly MEN2A, MEN2B)

ret proto-oncogene (multiple endocrine neoplasia and medullary thyroid carcinoma 1, Hirschsprung disease)

TGFA

transforming growth factor α

TGFB1

transforming growth factor β1 (Camurati-Engelmann disease)

TNF

tumor necrosis factor (TNF superfamily, member 2)

TNFRSF1A

TNF receptor superfamily, member 1A

TP53

tumor protein p53 (Li-Fraumeni syndrome)

15.3, Cardiology

ANK2 (formerly LQT4)

ankyrin 2 (neuronal; formerly long QT syndrome 4)

APOA1

apolipoprotein AI

APOB

apoliprotein B

APOC2

apoliprotein CII

APOD

apoliprotein D

APOE

apolipoprotein E

GPR1

G protein–coupled receptor 1

HDLBP

high-density lipoprotein-binding protein (vigilin)

KCNH2 (formerly LQT2)

potassium voltage-gated channel, subfamily H (eag-related), member 2

KCNQ1 (formerly LQT1)

potassium voltage-gated channel, KQT-like subfamily, member 1

LDLR

low-density lipoprotein receptor (familial hypercholesterolemia)

LPL

lipoprotein lipase

NOS1

nitric oxide synthase 1 (neuronal)

NOS2A

nitric oxide synthase 2A (inducible, hepatocytes)

NOS2B

nitric oxide synthase 2B

NOS2C

nitric oxide synthase 2C

NOS3

nitric oxide synthase 3 (endothelial cell)

PLAT

tissue plasminogen activator

SCN5A (formerly LQT3)

sodium channel, voltage-gated, type V, alpha polypeptide (long QT syndrome 3)

TNNC1

troponin C, slow

TNNC2

troponin C2, fast

TNNI1

troponin I, skeletal, slow

TNNC2

troponin C2, fast

TNNI1

troponin I, skeletal, slow

TNNI2

troponin I, skeletal, fast

TNNI3

troponin I, cardiac

TNNT1

troponin T1, skeletal, slow

TNNT2

troponin T2, cardiac

TNNT3

troponin T3, skeletal, fast

VLDLR

very-low-density lipoprotein receptor

15.7, Hemostasis

A2M

α2-macroglobulin

CALM1

calmodulin 1 (phosphorylase kinase, δ subunit)

CCL5

chemokine (C-C motif), ligand 5

CLEC3B (was TNA)

C-type lectin domain family 3, member B

F2

coagulation factor II (thrombin)

F2R

coagulation factor II (thrombin) receptor

F2RL1

coagulation factor II (thrombin) receptorlike 1

F3

coagulation factor III (tissue factor, thromboplastin)

F5

coagulation factor V

F7

coagulation factor VII

F7R

coagulation factor VII regulator

F8

coagulation factor VIII, procoagulant component (hemophilia A)

F8A1

coagulation factor VIII associated (intronic transcript) 1

F9

coagulation factor IX

F10

coagulation factor X

F11

coagulation factor XI

F12

coagulation factor XII

F13A1

coagulation factor XIII, A1 polypeptide

F13A2

coagulation factor XIII, A2 polypeptide

F13B

coagulation factor XIII, B polypeptide

FGA

fibrinogen A, α polypeptide

FGB

fibrinogen B, β polypeptide

FGG

fibrinogen, γ polypeptide

FGL1

fibrinogenlike 1

FGL2

fibrinogenlike 2

GP5

glycoprotein V (platelet)

GP6

glycoprotein VI (platelet)

GP9

glycoprotein IX (platelet)

GP1BA

glycoprotein Ib, (platelet), α-polypeptide

ICAM1

intercellular adhesion molecule 1 (CD54)

ICAM2

intercellular adhesion molecule 2

ITGA1

α1 integrin

ITGA2

α2 integrin

ITGA2B

α2b integrin (platelet glycoprotein [Gp] IIb of IIb/IIIa complex, antigen CD41B)

ITGA3

α3 integrin

ITGA6

α6 integrin

ITGAV

αv integrin (vitronectin receptor, a polypeptide, antigen CD51)

ITGB1

β1 integrin (fibronectin receptor,β polypeptide, antigen CD29)

ITGB3

integrin (platelet GpIIIa, antigen CD61)

ITPKA

inositol 1,4,5-triphosphate (IP3) A

KLKB1

kallikrein B, plasma

KNG1

kininogen 1

NOS3

nitric oxide synthase 3 (endothelial cell)

PDGFA

platelet-derived growth factor α-polypeptide

PDGFC

platelet-derived growth factor C

PDGFRA

platelet-derived growth factor receptor, α-polypeptide

PDGFRL

platelet-derived growth factor receptor–like

PECAM1

platelet/endothelial cell adhesion molecule (CD31 antigen)

PLAT

plasminogen activator, tissue (tPA)

PLAU

plasminogen activator, urokinase (uPA)

PLAUR

uPA receptor

PLG

plasminogen

PLGLA1

plasminogenlike A1

PLGLB1

plasminogenlike B1

PPBP

proplatelet basic proteins (includes β-thromboglobulin)

PROC

protein C

PROS1

protein S

PROSP

protein S pseudogene

PROZ

protein Z, vitamin K–dependent plasma glycoprotein

PTGDR

prostaglandin D2 receptor

PTGDS

prostaglandin D2 synthase

PTGFR

prostaglandin F receptor

PTGFRN

prostaglandin F2 receptor negative regulator

PTGIR

prostaglandin I2 (prostacyclin) receptor

PTGIS

prostaglandin I2 (prostacyclin) synthase

PTGS1

prostaglandin-endoperoxide synthase 1 (prostaglandin G/H synthase and cyclo-oxygenase)

SELE

E-selectin (endothelial adhesion molecule 1)

SELP

P-selectin

SERPINA1

serine (or cysteine) proteinase inhibitor, clade A (α1-antiproteinase, antitrypsin), member 1

SERPINC1

serine (or cysteine) proteinase inhibitor, clade C (antithrombin), member 1

SERPINE1

serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1

SERPINF2

serine (or cysteine) proteinase inhibitor, clade F (α2-antiplasmin, pigment epithelium derived factor), member 2

TBXA2R

thromboxane A2 receptor

TBXAS1

thromboxane A synthase 1

TFPI

tissue factor pathway inhibitor

TFPI2

tissue factor pathway inhibitor 2

THBD

thrombomodulin

VCAM1

vascular cell adhesion molecule 1

VWF

von Willebrand factor

VWFP

von Willebrand factor pseudogene

15.8, Immunology

15.8.1, Chemokines

CCL1

CCL1

CX3CL1

CX3CL1

CXCL1

CXCL1

PF4

platelet factor 4 (CXCL4)

XCL1

XCL1

15.8.2, CD Cell Markers

CD14

CD14 antigen

CD19

CD19 antigen

CD1A

CD1a

CD3D

CD3δ

CD46(was MCP)

complement regulatory protein, CD46

CD55, (was DAF) for complement (Cromer blood group system)

CD6

CD6

CD6

CD79A

CD79A, Igα

CD97

CD97

CR1

complement receptor type 1, CD35

FCGR3A

FcγRIIIa, CD16

ICAM3

intracellular adhesion molecule 3, CD50

MME

membrane metalloendopeptidase, CD10, CALLA

15.8.3, Complement

C1QA

C1qα

C1QB

C1qβ

C1QBP

C1qbp

C1QR1

C1qR1

C1R

C1r

C1S

C1s

C2

C2

C3

C3

C4A

C4a

C4B

C4b

C4BPA

C4bp-α

C5

C5

C5AR1

C5aR1

C6

C6

C7

C7

C8A

C8α

C8B

C8β

C9

C9

CD55 (was DAF)

CD 55, DAF for complement (Cromer blood group system)

CFH

complement factor H

CFP

complement factor properdin

15.8.4, Cytokines

CRLF1

cytokine receptorlike factor 1

CRLF2

cytokine receptorlike factor 2

CSF1

M-CSF

CSF2

GM-CSF

CSF3

G-CSF

CSF3R

G-CSF receptor

EPO

erythropoeitin (Epo)

EPOR

Epo receptor

GH1

growth hormone (GH) 1

GH2

GH 2

GHR

GH receptor

IFNA1

IFN-α1

IFNA2

IFN-α2

IFNB1

IFN-β1

IFNG

IFN-γ

IFNW1

IFN-α

IL1A

IL-1α

IL1B

IL-1β

IL1R1

IL-1RI

IL1R2

IL-1RII

IL1RAP

IL-1R accessory protein

IL1RN

IL-1 receptor antagonist (IL-1ra)

IL2

IL-2

LEP

leptin

LEPR

leptin receptor

PRL

prolactin

SOCS1

suppressor of cytokine signaling 1

TGFA

transforming growth factor α (TGF-α)

TGFB1

TGF-β1 (Camurati-Engelmann disease)

THPO

thrombopoietin

TNF

tumor necrosis factor (TNF superfamily member 2)

15.8.5, HLA/Major Histocompatibility Complex

HLA-A

HLA-A

HLA-B

HLA-B

HLA-C

HLA-C

HLA-DMA

HLA-DM α

HLA-DMB

HLA-DM β

HLA-DOA

HLA-DO α

HLA-DOB

HLA-DOβ

HLA-DPA1

HLA-DP α1

HLA-DQA1

HLA-DQ α1

HLA-DQB1

HLA-DQ β1

HLA-DRA

HLA-DR α

HLA-DRB1

HLA-DRβ1

HLA-E

HLA-E

HLA-F

HLA-F

HLA-G

HLA-G

HLA-H

HLA-H (pseudogene)

HLA-J

HLA-J (pseudogene)

15.8.6, Immunoglobulins

IGHA1

Cα1

IGHA2

Cα2

IGHD

Cδ

IGHD1-1

DH1 subgroup member 1

IGHE

Cε

IGHG1

Cγ1

IGHG2

Cγ2

IGHG3

Cγ3

IGHG4

Cγ4

IGHJ1

JH1

IGHM

IgM μ CH

IGHV@

VH

IGHV1-2

VH1 subgroup member 2

IGHV1-18

VH1 subgroup member 18

IGKC

Cκ

IGKJ@

Jκ

IGKJ2

Jκ2

IGKV@

Vκ

IGKV1-5

Vκ1 subgroup member 5

IGLC@

Cλ

IGLC1

Cλ1

IGLJ@

Jλ

IGLJ1

Jλ1

IGLV@

Vλ

IGLV10-54

Vλ10 subgroup member 54

15.8.7, Lymphocytes

TRAC

T-cell receptor α chain (TCRα)

TRBC1

TCRβ1

TRBC2

TCRβ2

TRBV10-3

TCRβ variable 10 subgroup member 3

TRGC1

TCRγ C1

TRGJ1

TCRγ J1

TRGJ2

TCRγ J2

TRDC

TCRδ C

15.10, Molecular Medicine

APBA1

amyloid-β peptide precursor

ADIPOQ

adiponectin (Acrp30), C1Q and collagen domain containing

ADIPOR1

adiponectin receptor 1

ADIPOR2

adiopnectin receptor 2

ACSL1

acyl-CoA synthetase long-chain family member 1

ADAMTS1

ADAM metallopeptidase with thrombospondin type 1 motif, 1

AHCY

S-adenosylhomocysteine (adoHcy)

AMD1

adenosylmethionine decarboxylase 1

AKT1

ν-akt murine thymoma viral oncogene homolog 1

ATP1A1

ATPase, Na+/K+ transporting, alpha 1 polypeptide

BPGM

2,3-bisphosphoglycerate mutase

CALM1

calmodulin 1

CCAR1

cell division cycle and apoptosis regulator 1

CCPG1

cell cycle progression 1

CCRK

cell cycle–related kinase

CDC2

cell division cycle 2, G1 to S and G2 to M

CDCA1

cell division cycle–associated 1

CDK2

cyclin-dependent kinase (DCK) 2

CDK7

CDK-activating enzyme (CAK) cyclinH/CDK7

CDKN1A

CDK inhibitor 1A (p21)

CDKN1C

CDK inhibitor 1C (p57)

CDKN2A

cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4 [p16Ink4a])

COASY

Coenzyme A (CoA) synthetase

COX4I1

cytochrome c oxidase subunit IV isoform 1

COX5B

Cytochrome c oxidase subunit νb

CRP

C-reactive protein, pentraxin-related

CYP1A2

cytochrome P450 1A2 isozyme (CYP1A2)

DHFR

dihydrofolate reductase

DKK1

Dickkopf homolog 1

ERBB2

v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuroblastoma-/glioblastoma-derived oncogene homolog (avian) (formerly HER2/neu)

FBP1

fructose 1,6-bisphosphatase 1

FDX1

ferredoxin (Fd) 1

FDX2

Fd 2

FHIT

fragile histidine triad (Fhit) gene

GNA12

G protein Gα12

GNG2

Gγ2

GALNT1

GalNAc transferase 1

G6PD

glucose-6-phosphate dehydrogenase

B3GALT1

UDP-Gal:β-GlcNAcβ-1,3-galactosyltransferase, polypeptide 1

CDKN2A

CDK4 inhibitor 2A

GFI1

growth factor independent 1

GRB2

growth factor receptor-bound protein 2

GRIN1

glutamate receptor, inotropic, N-methyl-d-aspartate (NMDA) 1

HBA1

hemoglobin (Hb) α1

HBB

Hbβ

HMGCS1

3-hydroxy-3-methylglutaryl CoA synthase 1

IGF1

insulinlike growth factor 1 (IGF-1)

IGF1R

IGF-1 receptor (IGF-R1)

IKBKB

IκB kinase β (IKKβ)

ITPKA

inositol 1,4,5-triphosphate (IP3) A

MNAT1

menage a trois 1 (CAK assembly factor)

MB

myoglobin (Mb)

MCM2

Mcm 2 minichromosome maintenance deficient 2, mitotin (Saccharomyces cerevisiae)

NMNAT1

nicotinamide nucleotide adenyltransferase 1

NPY

neuropeptide

NPPA

natriuretic peptide precursor α

OGDH

oxoglutarate (a-ketoglutarate) dehydrogenase (lipoamide)

PIB5PA

phosphatidylinositol 4,5-biphosphate (PIP2) 5-phosphatase A

PYY

peptide YY

RBBP4

retinoblastoma binding protein 4

RNASE1

ribonuclease, RNase A family 1 (pancreatic)

SFPQ

splicing factor proline/glutamine-rich

SNCA

α-synuclein

TAF1

TAF1 RNA polymerase II, TATA box binding protein (TBP)–associated factor

TBP

TATA box binding protein

THPO

thrombopoietin

TNFSF11 (alias: RANKL)

TNF (ligand) superfamily member 11

TP53

tumor protein p53

UCP1

uncoupling protein 1 (UCP-1)

WNT1

wingless-type mouse mammary tumor virus (MMTV) integration site family, member 1

15.11, Neurology

ACCN1

amiloride-sensitive cation channel 1, neuronal

ACHE

acetylcholinesterase (Yt blood group)

ADORA1

adenosine A1 receptor

ADRA1A

α1A-adrenergic receptor

ADRB1

β1-adrenergic receptor

BDNF

brain-derived neurotrophic factor

CACNA1A

Ca2+, voltage-dependent, P/Q type, α1A subunit

CHRM1

cholinergic receptor, muscarinic 1

CHRNA1

cholinergic receptor, nicotinic, α-polypeptide 1 (muscle)

CNTF

ciliary neurotrophic factor

COMT

catechol-O-methyltransferase

DRD1

dopamine receptor D1

EGF

epidermal growth factor

GABBR1

γ-aminobutyric acid (GABA) B receptor 1

GDNF

glial cell line–derived neurotrophic factor

GRIA1

glutamate receptor, inotropic, α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) 1

GRIN1

glutamate receptor, NMDA 1

HRH1

histamine receptor 1

HTR1A

serotonin (5-hydroxytryptamine) receptor 1A

ITPKA

inositol 1,4,5-triphosphate (IP3)A

KCNJ3(formerly GIRK1)

potassium inwardly rectifying channel, subfamily J, member 3

MAOA

monoamine oxidase A

NGFB

nerve growth factor β-polypeptide

NGFR

nerve growth factor receptor

NMB

neuromedin B

NOS1

nitric oxide synthase 1 (neuronal)

NPY

neuropeptide Y

NPY1R

neuropeptide Y receptor Y1

NRTN

neurturin NTF3 neurotrophin 3

NTS

neurotensin

NTSR1

neurotensin receptor 1

OPRD1

opioid δ receptor

OPRK1

opioid κ receptor

OPRM1

opioid m receptor OPRS1 opioid receptor σ1

PCP2

Purkinje cell protein 2

SLC1A1(formerly EAAT3)

solute carrier family 1

SLC18A1

solute carrier family 18 (vesicular monoamine), member 1

SNAP25

synaptosomal-associated protein, 25 kDa

SNCA

a-synuclein

TAC1

tachykinin, precursor 1 (substance K, substance P, neurokinin 1, neurokinin 2, neuromedin L, neurokinin a, neuropeptide K, neuropeptide γ)

TAC3

tachykinin 3 (neuromedin K, neurokinin β)

TRPA1

transient receptor potential cation channel, subfamily A, member 1

TSNARE1

t-SNARE domain containing 1 [see 15.11, Neurology, for expansion]

VAMP1

vesicle-associated membrane protein 1 (synaptobrevin 1)

15.14.3 and 15.4.4, Virus and Prion Nomenclature

AAVS1

adeno-associated virus integration site 2

BNIP1

BLC2/adenovirus E1B 19kDa interacting protein 1

CR2

complement component (3d/Epstein-Barr virus receptor 2)

CXADR

coxsackievirus and adenovirus receptor

CXB3S

coxsackievirus B3 sensitivity

E11S

echovirus (serotypes 4, 6, 11, 19) sensitivity

EBI2

Epstein-Barr virus–induced gene 2

EBVM1

Epstein-Barr virus modification site 1

EBVS1

Epstein-Barr virus insertion site 1

HAVCR1

hepatitis A virus cellular receptor 1

HBXAP

hepatitis B virus X-associated protein

HBXIP

hepatitis B virus X-interacting protein

HCVS

human coronavirus sensitivity

HIVE1

human immunodeficiency virus 1 (HIV-1) expression (elevated) 1

HPV6AI1

human papillomavirus type 6a integration site 1

HTLF

human T-cell leukemia virus enhancer factor

HV1S

herpes simplex virus type 1 sensitivity

ICAM1

intercellular adhesion molecule 1 (CD54), human rhinovirus receptor

MX1

myxovirus (influenza virus) resistance 1

PVR

poliovirus receptor

PRND

prion protein 2 (dublet)

PRNP

PrP27-30 (Creutzfeld-Jakob disease, Gerstmann-Strausler-Scheinker syndrome, fatal familial insomnia)

PRNPIP

prion protein interacting protein

PRNT

prion protein testis specific

Alleles.

Alleles denote alternative forms of a gene. Alleles are often characterized by particular variant sequences (mutations). For variant sequence nomenclature see “Sequence Variations, Nucleotides, and Sequence Variations, Amino Acids,” in 15.6.1, Nucleic Acids and Amino Acids.

Because alleles are alternative forms of a particular gene, they are expressed by means of both the gene name or symbol and an appendage that indicates the specific allele.

Classically, allele symbols consist of the gene symbol plus an asterisk plus the italicized allele designation,7 eg:

HBB*S

S allele of the HBB gene

As with gene terms, Greek letters are changed to Latin letters in allele terms:

APOE*E4

allele producing the e4 type of apolipoprotein E

If clear in context, the allele symbol may be used in a shorthand form that omits the gene symbol and includes only the asterisk and the allele designation that follows, eg:

*S

*E4

In the case of alleles of the major histocompatibility locus, which are not italicized (see 15.8.5, Immunology, HLA/Major Histocompatibility Complex), a portion of the gene name is usually included in the shortened form:

Full Name

Shortened Form

HLA-DRB1*0301

DRB1*0301

In practice, common or trivial names for alleles, which take various forms, are used. The same allele is often expressed in different ways that diverge from the recommended nomenclature. For example:

s: short allele of serotonin transporter gene (SLC6A4)

l: long allele of SLC6A4

As another example of common allele names, the following expressions are all used for APOE*E4; follow author preference:

ε 4 allele

epsilon 4 allele

E4 allele

APOE*4

apo e4

APOEE4

A system of nomenclature that takes evolutionary divergence into account has been proposed for alleles.12 Stylistically, it is consistent with the above system of nomenclature, ie, asterisk followed by italicized alphanumeric allele designator. Examples (from Nebert12):

NAT2*4

*1A1

*3A3

*7A28T17L47B88

Genotype and Phenotype Terminology

The genotype comprises the set of alleles in an individual. Because individuals almost always have 2 of each autosome (nonsex chromosome) (see 15.6.4, Human Chromosomes), individuals have 2 alleles (which may be the same alleles or 2 different alleles) for each autosomal gene.

The simplest genotype term for an individual would describe 1 gene and consist of the names of 2 alleles. Larger genotypes would contain 2 or more allele symbol pairs.

As originally formulated in ISGN, allele groupings may be indicated by placement above and below a horizontal line or on the line. As seen in the following examples (from Shows et al2,3), such placement, as well as order, spacing, and punctuation marks (virgules [/], semicolons, spaces, and commas), has specific meanings.

Alleles of the same gene are indicated by placement above and below a horizontal line or with a virgule:

ADA1ADA2orADA1/ADA2

In theoretical discussions when a single letter is substituted for the allele symbol, the line or virgule may be dispensed with:

AA

Aa

aa

ss

ll

sl

Semicolons separate pairs of alleles at unlinked loci:

ADA1ADA2;ADH11ADH11;AMY1AAMY1B

or

ADA*1/ADA*2; ADH1*1/ADH1*1; AMY1*A/AMY1*B

or

ADA*1/*2; ADH*1/*1;AMY1*A/*B

A single space separates alleles together on the same chromosome from alleles together on another chromosome (phase known):

AMY1APGM12AMY1BPGM11

or

AMY1*A PGM1*2/AMY1*B PGM1*1

Commas indicate that alleles above and below the line (or on either side of the virgule) are on the same chromosome pair, but not on which chromosome of the pair specifically (phase unknown):

PGM11PGM12,AMY1AAMY1B

or

PGM1*1/PGM1*2, AMY1*A/AMY1*B

A special form for hemizygous males is

G6PD*A/Y

When genotype is being expressed in terms of nucleotides (eg, a polymorphism), italics and other punctuation are not needed (see also 15.6.1, Nucleic Acids and Amino Acids):

MTHFR677 TT genotype

CC genotype

the “long/short” (5HTTLPR) polymorphism in SLC6A4

(LPR: length polymorphism region)

When the subject is being described in terms of the 2 possible amino acids at 1 position in the protein owing to a single nucleotide polymorphism (nonsynonymous mutation), the corresponding amino acids are separated by a virgule (see also 15.6.1, Nucleic Acids and Amino Acids):

Val/Val (homozygous)

Met/Val (heterozygous)

Met/Met (homozygous)

Such terms should be explained at first mention with the amino acid terms expanded:

the common methionine/valine (Met/Val) polymorphism at codon 129

The virgule is not needed in expressions such as the following:

α1-antitrypsin MZ heterozygotes

individuals with the ZZ phenotype

The phenotype is the collection of traits in an individual resulting from his or her genotype. When phenotypes are expressed in terms of the specific alleles, the phenotype term derives from the genotype term, but no italics are used, and, instead of asterisks, spaces are used. Genotypes usually contain pairs of symbols, while phenotypes contain single symbols. The following examples are from Shows et al3:

Genotype

Phenotype

ADA*1/ADA*1

ADA 1

ADA*1/ADA*2

ADA 1–2

C2*C/C2*QO

C2 C,QO

HBB*A/HBB*6V

HBB A,S [traditional, Hb A/S]

ABO*A1/ABO*O

ABO A1

CFTR*N/CFTR*R

CFTR N

G6PD*A/Y

G6PD A

NAT2*4/*4

rapid acetylator

CYP2D6*4A/*5

poor metabolizer

OMIM

Online Mendelian Inheritance in Man (OMIM) is a database of genetic syndromes.13 The site is located at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM.

When a specific syndrome is mentioned, it is helpful to include the OMIM number:

bronchomalacia (Online Mendelian Inheritance in Man [OMIM] 211450)

DiGeorge syndrome (OMIM #188400)

Explanation of symbols that precede many OMIM numbers (eg, #, *, or %) is found in the OMIM frequently answered questions (FAQs) site, http://www.ncbi.nlm.nih.gov/Omim/omimfaq.html#numbering_system, and in Hamosh et al.13

References

1. Klinger HP. Progress in nomenclature and symbols for cytogenetics and somatic-cell genetics. Ann Intern Med. 1979;91(3):487-488.Find this resource:

2. Shows TB, Alper CA, Bootsma D, et al. International system for human gene nomenclature (1979). Cytogenet Cell Genet. 1979;25(1-4):96-116.Find this resource:

3. Shows TB, McAlpine PJ, Boucheix C, et al. Guidelines for human gene nomenclature: an international system for human gene nomenclature (ISGN, HGM9). Cytogenet Cell Genet. 1987;46(1-4):11-28.Find this resource:

4. Rangel P, Giovannetti J. Genomes and Databases on the Internet: A Practical Guide to Functions and Applications. Norfolk, England: Horizon Scientific Press; 2002.Find this resource:

    5. HUGO Gene Nomenclature Committee website. http://www.gene.ucl.ac.uk/nomenclature/. Updated March 29, 2006. Accessed April 21, 2006.

    6. Searchgenes. Human Gene Nomenclature Database Search Engine. http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/searchgenes.pl. Updated April 21, 2006. Accessed April 21, 2006.

    7. Wain HM, Bruford EA, Lovering RC, Lush MJ, Wright MW, Povey S. Guidelines for human gene nomenclature. Genomics. 2002;79(4):464-470. Also available at http://www.gene.ucl.ac.uk/nomenclature/guidelines.html. Updated April 20, 2006. Accessed April 21, 2006.Find this resource:

    8. Wain HM, Lush M, Ducluzeau F, Povey S. Genew: the Human Gene Nomenclature Database. Nucleic Acids Res. 2002;30(1):169-171.Find this resource:

    9. Wain HM, Lush MJ, Ducluzeau F, Khodiyar VK, Povey S. Genew: the Human Gene Nomenclature Database, 2004 updates. Nucleic Acids Res. 2004;32(database issue): D255-D257. doi:10.1093/nar/gkh072.Find this resource:

    10. Entrez Gene. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene. Accessed April 21, 2006.

    11. HGNC FAQs. http://www.gene.ucl.ac.uk/nomenclature/information/FAQs.html. Updated April 20, 2006. Accessed April 24, 2006.

    12. Nebert DW. Proposal for an allele nomenclature system based on the evolutionary divergence of haplotypes. Hum Mutat. 2002;20(6):463-472.Find this resource:

    13. Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucl Acids Res. 2005;33(database issue):D514-D517. doi:10.1093/nar/gki033.Find this resource:

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