ASHG01 Nomenclature Workshop (ASHG01-NW)

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Friday October 12, 2001
San Diego
The Convention Center - Room 14A


14:00 - 14:30
Introduction of Proposed Guidelines
14:30 - 15:30
Discussion of Guidelines
15:30 - 16:00
16:00 - 17:30
Further Discussion of Guidelines
17:30 - 18:00
Agreement of Proposed Guidelines and alterations


Summary of "The Proposal of New Human Gene Nomenclature Guidelines"


Cindy Smith (MGD), Hester Wain (HGNC), Sue Povey (HGNC), Elspeth Bruford (HGNC), Cara Hunsberger (Molecular Therapy and Genomics), Donna Maglott (NCBI/LocusLink), Stephen Scherer (HGAC), Panos Deloukas (Sanger), Gerard Manning (Kinases, Sugen), Chris Porter (GDB), Alan Scott (OMIM), Kim Pruitt (Ref_Seq), Lucy Osborne (WBS Region), Lap-Chee Tsui (HUGO).

Updates from this meeting have now been incorporated into the guidelines.

A list of the issues discussed and actions recommended is detailed below:

Draft Guidelines for Human Gene Nomenclature - 2001

The Draft Guidelines were updated on 17 and 21 September and 3 October 2001, updates shown in red; recent updates (1 November) from the workshop and other sources are shown inpink 
Please note that not all browsers support the fonts used in this document, this is particularly pertinent when viewing the Greek-Latin letter conversion table.


Guidelines for human gene nomenclature were first published in 1979 by Shows et al. when the Human Gene Nomenclature Committee was first given the authority to approve and implement human gene names and symbols. Updates of these guidelines were published in 1987 (Shows et al.), 1995 (McAlpine P) and 1997 (White et al.). With the recent publications of the complete human genome sequence there is an estimated total of 26,000-40,000 genes, as suggested by the International Human Genome Sequencing Consortium (2001) and Venter et al. (2001). Thus, the guidelines have been updated to accommodate their application to this wealth of information although symbols are still only assigned when required for communication about genes.

The philosophy of the HGNC remains "that gene nomenclature should evolve with new technology rather than be restrictive as sometimes occurs when historical and single gene nomenclature systems are applied" (Shows et al 1987).


1. Each approved gene symbol must be unique.
2. Symbols are short-form representations (or abbreviations) of the descriptive gene name.
3. Symbols should only contain Latin letters and Arabic numerals.
4. Symbols should not contain punctuation.
5. Symbols should not end in "G" for gene.
6. Symbols do not contain any reference to species e.g. "h" for human.

1. Criteria for symbol assignment

A gene is defined as: "a DNA segment that contributes to phenotype/function. In the absence of demonstrated function a gene may be characterized by sequence, transcription or homology".  The overwhelming majority of objects named by HGNC are in this category.

The word locus is not a synonym for gene and refers to a map position. A more precise definition is given in the Rules and Guidelines from the International Committee on Standardized Genetic Nomenclature for Mice which states: "A locus is a point in the genome, identified by a marker, which can be mapped by some means. It does not necessarily correspond to a gene; it could, for example, be an anonymous non-coding DNA segment or a cytogenetic feature. A single gene may have several loci within it (each defined by different markers) and these markers may be separated in genetic or physical mapping experiments. In such cases, it is useful to define these different loci, but normally the gene name should be used to designate the gene itself, as this usually will convey the most information."

Chromosome Region
In the context of gene nomenclature this is defined as a genomic region which has been associated with a particular syndrome or phenotype, particularly when there is a possibility that several genes within it may be involved in the phenotype. Designation of such regions may be requested by the scientific community and approved by HGNC e.g.  etc. ANCR "Angelman syndrome chromosome region" and CECR "cat eye syndrome chromosome region".

Symbols may therefore be assigned to the following:

Gene symbols will not usually be assigned to alternative transcripts or to genes predicted solely from in silico data (with no other supporting evidence e.g. significant homology to a characterised gene).

2. Gene symbols

Human gene symbols are designated by upper-case Latin letters or by a combination of upper-case letters and Arabic numerals, with the exception of the C#orf# symbols. Symbols should be short in order to be useful, and should not attempt to represent all known information about a gene (White et al. 1998). Symbols should be inoffensive and should not spell words or match abbreviations that would cause problems with database searching e.g. DNA. Ideally, symbols should be no longer than six characters in length. New symbols must not duplicate existing approved gene symbols in either the human (Genew: Human Gene Nomenclature Database) or the mouse (MGD) databases.

3. Gene names

Gene names should be brief and specific and should convey the character or function of the gene, but should not attempt to describe everything known about it. The first letter of the symbol should be the same as that of the name in order to facilitate alphabetical listing and grouping. Gene names are written using American spelling. Tissue specificity and molecular weight designations should be avoided as they have only limited use as a description and may in time and across species prove inaccurate; however, they may be incorporated into the gene name if absolutely necessary. Gene names should not include terms such as nephew, cousin, sister etc. to describe familial relationships with other genes.  The following gene name syntax should be used:

4. Gene Families

Hierarchical symbols for both structural and functional gene families should be used where possible. A stem (or root) symbol as a basis for a symbol series allows easy identification of other family members in both database searches and the literature. Gene family members should be designated by Arabic numerals placed immediately after the gene stem symbol, without any space between the letters and numbers used e.g. GPR1, GPR2, GPR3 (three G protein-coupled receptor genes ). However, very occasionally, only if they exist historically, single-letter suffixes may be used to designate these different genes e.g. LDHA, LDHB, LDHC (three lactate dehydrogenase genes). Some gene families are very large and so may include a variety of number/letter combinations to indicate their phylogenetic relationships e.g. CYP1A1, CYP21A2, CYP51A1 (three members of the cytochrome P450 superfamily).  When symbols are approved by the HGNC consecutively in a gene family the hierarchical order of symbols will not necessarily reflect the chronological order of peer-reviewed publications.  Consecutive symbols approved by HGNC take precedence over those published, although this will be a matter for discussion with the relevant scientific community.

Many genes receive approved symbols and names which are non-ideal when considered in the light of subsequent information.  In the case of individual genes a change to the name (and subsequently the symbol)  is only made if the original name is seriously misleading. However, groups of scientists working on particular gene families often co-ordinate a revised nomenclature when more information becomes available; such initiatives are welcomed. Groups planning to do this are strongly advised to liase with the HGNC in order to avoid possible problems. Previously approved symbols which have been withdrawn should not be re-used as this causes great confusion in information retrieval.

Anonymous families
When a series of genes can be shown to be related by sequence similarity but otherwise cannot be described by homology or function they can be assigned anonymous and temporary FAM# symbols. Membership in each family, indicated by the FAM number, will be assigned using the general criteria established by Mackenzie et al. (1997) and Nelson et al. (1996): that the gene products show greater than 40% amino acid identity. However, these criteria are not exclusive but merely a convenient starting point on which to base an appropriate symbol. The symbol will always include a letter designation for sub-family, with the final character indicating gene number e.g. FAM7A1 "family with sequence similarity 7, member A1" etc. Once further information is available to assign a more descriptive name the whole gene family should be updated with new symbols; the FAM designations being withdrawn.

5. Homologies with other species

Homologous genes in different vertebrate species (orthologs) should where possible have the same gene nomenclature.

6. Genes identified from sequence information

A gene of unknown function, encoded at the same genomic locus (with overlapping exons) as another gene should have its own symbol.  If the new gene regulates the first gene it may be assigned the symbol of the first gene with the suffix AS for antisense e.g. IGF2AS "insulin-like growth factor 2, antisense". The gene symbol should not be written backwards.

Opposite Strand
Genes of unknown function on the opposite strand, which have no proven regulatory function, should be assigned the suffix OS for "opposite strand".

Untranslated Functional RNAs
These may be assigned symbols that are unique and relevant to the scientific community. However, the approved name should contain "untranslated RNA" e.g. H19 "H19, imprinted maternally expressed untranslated RNA".

Related (-like) sequences
The designation of the suffix "L" for like has been used in the past for related sequences identified by cross-hybridisation studies. Where genes are identified by database searching and where no other functional information is available and there is some sequence similarity with a known gene they are designated with the symbol of the known gene followed by an "L" for like e.g. ACY1L  "aminoacylase 1-like".  Alternatively, if there are a number of similar genes they may be assigned numbers in a series e.g. BTNL1 "butyrophilin-like 1" to BTNL3.

Genes of unknown function
Genes predicted from EST clusters or from genomic sequence with EST evidence, but showing no structural or functional homology, are regarded as putative. These are designated by the chromosome of origin, the letters orf for open reading frame and a number in a series e.g. C2orf1, "chromosome 2 open reading frame 1". The use of the lower case letters "orf" is to prevent confusion between the first letter "o" and the numeral "0" (zero), which may be part of the chromosome number.

Pseudogenes are sequences that are generally untranscribed and untranslated and which have high homology to identified genes . However, it has recently been shown that in different organisms or tissues functional activation may occur. Therefore, the previous policy of assigning the gene symbol of the structural gene followed by "P" and a number will only be approved on a case by case basis. In future, pseudogenes will usually be assigned the next number in the relevant symbol series, suffixed by a "P" for pseudogene if requested e.g. OR5B12P"olfactory receptor, family 5, subfamily B, member 12 pseudogene". However, the designation pseudogene will remain in the gene name.

7. Enzymes and proteins

The rules described in the sections on gene names and symbols apply, but in addition the names of genes coding for enzymes should be based on those recommended by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology e.g. FPGS "folylpolyglutamate synthase". These can be found at URL <>. Names of genes encoding plasma proteins, hemoglobins, and specialised proteins are based on standard names and those recommended by their respective committees e.g. HBA1 "hemoglobin, alpha 1".

8. Clinical disorders

The first gene symbol allocated to an inherited clinical phenotype (monogenic Mendelian inheritance) may be based on an acronym which has been established as a name for the disorder, whilst following the rules described previously e.g. ACH for "achondroplasia". It is usual for this symbol to change when the gene product or function is identified; however, if there is no additional information derived from the cloned gene, the disease symbol e.g. ACHwill be maintained. If an approved gene symbol for the cloned gene based on product or function already exists this will take precedence over the symbol derived from the clinical disorder when the gene descriptions are merged. For example, in the case of achondroplasia the symbol ACH was withdrawn and FGFR3 and the name "fibroblast growth factor receptor 3 (achondroplasia, thanatophoric dwarfism)" approved in its place. If the original symbol is to be maintained we do not recommend the sole use of invented names based upon the phenotype e.g. tuberin for TSC2 "tuberous sclerosis 2".

Complex/polygenic traits
Genome searches may suggest a contributing locus in a complex trait, which may for convenience be given a gene symbol e.g. IDDM3 "insulin-dependent diabetes mellitus 3", although a proportion of these will disappear in time. A symbol allocated to such a locus will not be re-used.

Contiguous gene syndromes
Syndromes clearly associated with multiple widely dispersed loci should not be given gene symbols. Syndromes associated with a regional deletion or duplication may be assigned the letters CR (for chromosome region), in place of S for syndrome. Examples include ANCR  "Angelman syndrome chromosome region", CECR "cat eye syndrome chromosome region". However, as advances in database design have increased the possible ways of representing this type of information, we recommend that such symbols are classified as syndromic region symbols and not gene symbols. Candidate genes found within a chromosomal region may be assigned a symbol based on the syndromic region symbol with sequential numbering e.g. CECR1 "cat eye syndrome chromosome region, candidate 1".

Loss of heterozygosity
A chromosomal region in which the existence of genes may be inferred by loss of heterozygosity can be designated by a symbol consisting of the letters LOH for loss of heterozygosity, the chromosome number, CR (for chromosomal region) and then a sequential number e.g. LOH1CR1 "loss of heterozygosity, 1, chromosomal region 1".

9. Genomic Rearrangements and Features

Genes only found within subsets of the population
Symbols will be assigned to genes generated by recombination events. The symbols will be designated a number or letter in the series determined from the original gene symbol e.g. KIR2DL5 gene is duplicated in some haplotypes, the original gene will be referred to as KIR2DL5A  "killer cell immunoglobulin-like receptor, two domains, long cytoplasmic tail, 5A" and the duplication as KIR2DL5B  "killer cell immunoglobulin-like receptor, two domains, long cytoplasmic tail, 5B". Information detailing position on the chromosome e.g. telomeric etc may be added to the gene name to aid understanding.  These types of symbols will be agreed on an individual basis.

Gene recombination
When there has been recombination between genes, generating a new locus, the gene symbol should remain short but reflect the two (or more) initial gene symbols. The name may be as descriptive as necessary e.g. POMZP3 "POM (POM121 rat homolog) and ZP3 fusion".

Functional Repeat sequences
Sequence data for these records must be obtained by HGNC prior to symbol approval. Endogenous retroviruses have the stem symbol ERV, followed by a letter representing type and the next consecutive number in the series e.g. ERVK2 "endogenous retroviral sequence K(C4), 2". Transposable elements have the stem symbol TE, followed by a relevant character set e.g. MAR, and the next consecutive number in the series. Thus, a mariner-type transposable element could be TEMAR1 "transposable element mariner-type, 1". LINEs (Long Interspersed Nuclear Elements) are currently assigned the next consecutive number in the LRE series e.g. LRE1 "LINE retrotransposable element 1".

10. Characters reserved for specific usage

Letters, or combinations of letters are used as prefixes or suffices in a symbol to represent a specific meaning and so their use for other meanings should be avoided where possible (Table 1). The following letter usage is not acceptable; H or h for human, G or g for gene. If the name of a gene contains a character or property for which there is a recognized abbreviation, the abbreviation should be used e.g. the single-letter abbreviation for amino acids used in aminoacyl residues (App 2: Table 3). Other characters are also used within the symbol to represent genomic or genetic information (Table 1).

Table 1: Characters reserved for specific usage

Character Meaning
AS  antisense
AP  associated/accessory protein
BP  binding protein
C catalytic
CR chromosome/critical region
C#orf# chromosome # open reading frame #
D or DC domain containing
FAM family with sequence similarity
N or NH  inhibitor
IP  interacting protein
IT  intronic transcript 
LG ligand
LOH loss of heterozygosity
MT or M mitochondrial
OS opposite strand
OT  overlapping transcript
quantitative trait
RG  regulator
@ gene cluster in chromosomal region
# gene family

11. Symbol Status

Each gene record in the Genew database has one of five states:

Appendix 1: Gene symbol use in publications

It is recommended that gene and allele symbols are underlined in manuscript and italicized in print. Italics need not be used in gene catalogs. To distinguish between mRNA, genomic DNA and cDNA the relevant prefix should be written in parentheses (mRNA)RBP1, (gDNA)RBP1, (cDNA)RBP1.

DNA segments
These symbols can be obtained from The Genome Database (GDB) and are assigned automatically to arbitrary DNA fragments and loci. Please email requests to These symbols comprise five parts e.g. DXS9879E, described by the following guidelines
Part 1: D for DNA
Part 2: 0, 1, 2,...22, X, Y, XY for the chromosomal assignment, where XY is for segments homologous on the X and Y chromosomes, and 0 is for unknown chromosomal assignment.
Part 3: S, Z or F indicating the complexity of the DNA segment detected by the probe; with S for a unique DNA segment, Z for repetitive DNA segments found at a single chromosome site and F for small undefined families of homologous sequences found on multiple chromosomes.
Part 4: 1, 2, 3,..., a sequential number to give uniqueness to the above concatenated characters.
Part 5: When the DNA segment is known to be an expressed sequence the suffix E can be added to indicate this.

Allele terminology is the responsibility of the HUGO Mutation Database Initiative (now evolved into the Human Genome Variation Society) <>. However, alleles should still be limited to an optimum of three characters using only capital letters or Arabic numerals. The allele designation should be written on the same line as gene symbol separated by an asterisk e.g. PGM1*1, the allele is printed as *1. When only allele symbols are displayed an asterisk should precede them. Sequence variation nomenclature, in the form of mutations and polymorphisms, is described by Antonarakis et al (1998) and den Dunnen and Antonarakis (2001).  HLA alleles are assigned by the WHO Nomenclature Committee for Factors of the HLA System (Marsh et al 2001) via the IMGT/HLA database (Robinson et al. 2001). Immunoglobulin and T cell receptor alleles are assigned by the IMGT Nomenclature Committee via the IMGT/LIGM database (Lefranc 2001)".

Splice variants
The HGNC has no authority over protein nomenclature; however, we are frequently asked how to designate splice variants so we suggest the following:
Proteins should be designated using the same symbol as the gene, printed in non-italicized letters. When referring to splice variants, the symbol can be followed by an underscore and the lower case letter "v" then a consecutive number to denote which variant is which e.g. G6PD_v1.

Species designations
When necessary to distinguish the species of origin for homologous genes with the same gene symbol, the letter-based code for different species already established by SWISS-PROT should be used. This can be found at URL <> and commonly used species are shown in App 2: Table 2. The code is for use in publications only and should not be incorporated as part of the gene symbol. The species designation is added as a prefix to the gene symbol in parentheses. For example HUMAN signifies Homo sapiens and MOUSE signifies Mus musculus e.g. human genes: (HUMAN)ABCA1; (HUMAN)SLC13A2; homologous mouse genes: (MOUSE)Abca1; (MOUSE)Slc13a2.

Appendix 2: Tables

App 2: Table 1: Greek-to-Latin alphabet conversion

Greek Symbol Greek Latin upper 
case conversion 
a alpha 
b beta 
g gamma 
d delta 
e epsilon 
z zeta 
h eta 
q theta 
i iota 
k kappa 
l lambda 
m mu 
n nu 
x xi 
o omicron 
p pi 
r rho 
s sigma 
t tau 
u upsilon 
f phi 
c chi 
y psi 
w omega 

App 2: Table 2: Species Abbreviations from URL: <>

Common name Abbreviation Species
cat FELSI Felis silvestris catus
chicken CHICK Gallus gallus
chimp PANTR Pan troglodytes
dog CANFA Canis familiaris
fruit fly DROME Drosophila melanogaster
human HUMAN Homo sapiens 
mouse MOUSE Mus musculus
orangutan PONPY Pongo pygmaeus
pig PIG Sus scrofa
puffer fish FUGRU Fugu rubripes
puffer fish TETFL Tetraodon fluviatilis
rabbit RABIT Oryctolagus cuniculus
rat RAT Rattus norvegicus
worm CAEEL Caenorhabditis elegans
yeast YEAST Saccharomyces cerevisiae
yeast SCHPO Schizosaccharomyces pombe
zebrafish BRARE Brachydanio rerio

App 2: Table 3: Single-letter amino acid symbols

Amino acid  Three-letter 
Alanine  Ala 
Arginine  Arg 
Asparagine  Asn 
Aspartic acid  Asp 
Asn +Asp  Asx 
Cysteine  Cys 
Glutamine  Gln 
Glutamic acid  Glu 
Gln + Glu  Glx 
Glycine  Gly 
Histidine  His 
Isoleucine  Ile 
Leucine  Leu 
Lysine  Lys 
Methionine  Met 
Phenylalanine  Phe 
Proline  Pro 
Serine  Ser 
Threonine  Thr 
Tryptophan  Trp  W
Tyrosine  Tyr 
Valine  Val 


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