The HUGO Gene Nomenclature Committee (HGNC) has assigned unique gene symbols and names to almost 38,000 human loci, of which around 19,000 are protein coding. genenames.org is a curated online repository of HGNC-approved gene nomenclature and associated resources including links to genomic, proteomic and phenotypic information, as well as dedicated gene family pages.
The HGNC annotation database is a field database that, by default, annotates another gene name field such as refGene.name2, through its All_Symbols column, which contains all current and previously used gene names. For example, for gene TMEM261 with a previously used name C9orf123, it has two entries in the database,
name All_Symbols
TMEM261 TMEM261
TMEM261 C9orf123
so that the name field will have its HGNC approved name TMEM261. To link to this database, you should do, for example,
% vtools use HGNC --linked_by refGene.name2
INFO: Downloading annotation database from annoDB/HGNC.ann
INFO: Downloading annotation database from http://vtools.houstonbioinformatics.org/annoDB/HGNC-20131029.DB.gz
INFO: Using annotation DB HGNC in project test.
INFO: The HUGO Gene Nomenclature Committee (HGNC) has assigned unique gene symbols
and names to almost 38,000 human loci, of which around 19,000 are protein coding.
genenames.org is a curated online repository of HGNC-approved gene nomenclature and
associated resources including links to genomic, proteomic and phenotypic information,
as well as dedicated gene family pages
INFO: 22889 out of 23953 refgene.name2 are annotated through annotation database HGNC
WARNING: 30614 out of 53503 values in annotation database HGNC are not linked to the project.
Note that not all names in refGene have an entry in HGNC. Genes that are not in HGNC are mostly LOC????? genes. Then, instead of output refGene.name2, you can output HGNC approved name
% vtools output variant chr pos HGNC.name
You can, if you are interested, check the change of names using commands
% vtools select variant 'refGene.name2 != HGNC.name' --output chr pos refGene.name2 HGNC.name --all
although variants that belong to more than one gene will also be selected and outputted.
% vtools show annotation HGNC
Annotation database HGNC (version 20131029)
Description: The HUGO Gene Nomenclature Committee (HGNC) has
assigned unique gene symbols and names to almost 38,000 human loci, of which
around 19,000 are protein coding. genenames.org is a curated online
repository of HGNC-approved gene nomenclature and associated resources
including links to genomic, proteomic and phenotypic information, as well as
dedicated gene family pages
Database type: field
Reference genome *: All_Symbols
name HGNC Approved Symbol
All_Symbols All symbols, including Approved and repvious symbols
HGNC_ID A unique ID provided by the HGNC. In the HTML results
page this ID links to the HGNC Symbol Report for that
gene.
Approved_Symbol The official gene symbol that has been approved by the
HGNC and is publicly available. Symbols are approved
based on specific HGNC nomenclature guidelines. In the
HTML results page this ID links to the HGNC Symbol
Report for that gene.
Approved_Name The official gene name that has been approved by the
HGNC and is publicly available. Names are approved
based on specific HGNC nomenclature guidelines.
Status Indicates whether the gene is classified as: Approved
- these genes have HGNC-approved gene symbols Entry
withdrawn - these previously approved genes are no
longer thought to exist Symbol withdrawn - a
previously approved record that has since been merged
into a another record
Locus_Type Specifies the type of locus described by the given
entry: gene with protein product, RNA, cluster, etc (h
ttp://www.genenames.org/data/gdlw_columndef.html#gd_ap
p_sym)
Locus_Group Groups locus types together into related sets. See
http://www.genenames.org/data/gdlw_columndef.html#gd_a
pp_sym for details.
Previous_Symbols Symbols previously approved by the HGNC for this gene
Previous_Names Gene names previously approved by the HGNC for this
gene
Synonyms Other symbols used to refer to this gene
Name_Synonyms Other names used to refer to this gene
Chromosome Indicates the location of the gene or region on the
chromosome
Date_Approved Date the gene symbol and name were approved by the
HGNC
Date_Modified If applicable, the date the entry was modified by the
HGNC
Date_Symbol_Changed If applicable, the date the gene symbol was last
changed by the HGNC from a previously approved symbol.
Many genes receive approved symbols and names which
are viewed as temporary (eg C2orf#) or 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.
Date_Name_Changed If applicable, the date the gene name was last changed
by the HGNC from a previously approved name
Accession_Numbers Accession numbers for each entry selected by the HGNC
Enzyme_IDs Enzyme entries have Enzyme Commission (EC) numbers
associated with them that indicate the hierarchical
functional classes to which they belong
Entrez_Gene_ID Entrez Gene at the NCBI provide curated sequence and
descriptive information about genetic loci including
official nomenclature, synonyms, sequence accessions,
phenotypes, EC numbers, MIM numbers, UniGene clusters,
homology, map locations, and related web sites. In the
HTML results page this ID links to the Entrez Gene
page for that gene. Entrez Gene has replaced
LocusLink.
Ensembl_Gene_ID This column contains a manually curated Ensembl Gene
ID
Mouse_Genome_Database_ID MGI identifier. In the HTML results page this ID
links to the MGI Report for that gene.
Specialist_Database_Links This column contains links to specialist databases
with a particular interest in that symbol/gene (also
see Specialist Database IDs).
Specialist_Database_IDs The Specialist Database Links column contains HTML
links to the database in question. This column
contains the database ID only.
Pubmed_IDs Identifier that links to published articles relevant
to the entry in the NCBI's PubMed database.
RefSeq_IDs The Reference Sequence (RefSeq) identifier for that
entry, provided by the NCBI. As we do not aim to
curate all variants of a gene only one selected RefSeq
is displayed per gene report. RefSeq aims to provide a
comprehensive, integrated, non-redundant set of
sequences, including genomic DNA, transcript (RNA),
and protein products. RefSeq identifiers are designed
to provide a stable reference for gene identification
and characterization, mutation analysis, expression
studies, polymorphism discovery, and comparative
analyses.
Gene_Family_Tag Tag used to designate a gene family or group the gene
has been assigned to, according to either sequence
similarity or information from publications,
specialist advisors for that family or other
databases. Families/groups may be either structural or
functional, therefore a gene may belong to more than
one family/group. These tags are used to generate gene
family or grouping specific pages at genenames.org and
do not necessarily reflect an official nomenclature.
Each gene family has an associated gene family tag and
gene family description. If a particular gene is a
member of more than one gene family, the tags and the
descriptions will be shown in the same order.
Gene_family_description Name given to a particular gene family. The gene
family description has an associated gene family tag.
Gene families are used to group genes according to
either sequence similarity or information from
publications, specialist advisors for that family or
other databases. Families/groups may be either
structural or functional, therefore a gene may belong
to more than one family/group.
Record_Type
Primary_IDs
Secondary_IDs
CCDS_IDs The Consensus CDS (CCDS) project is a collaborative
effort to identify a core set of human and mouse
protein coding regions that are consistently annotated
and of high quality. The long term goal is to support
convergence towards a standard set of gene
annotations.
VEGA_IDs This contains a curated VEGA gene ID
Locus_Specific_Databases This contains a list of links to databases or
database entries pertinent to the gene
Entrez_Gene_ID_NCBI Entrez Gene at the NCBI provide curated sequence and
descriptive information about genetic loci including
official nomenclature, synonyms, sequence accessions,
phenotypes, EC numbers, MIM numbers, UniGene clusters,
homology, map locations, and related web sites. In the
HTML results page this ID links to the Entrez Gene
page for that gene. Entrez Gene has replaced
LocusLink.
OMIM_ID_NCBI Identifier provided by Online Mendelian Inheritance in
Man (OMIM) at the NCBI. This database is described as
a catalog of human genes and genetic disorders
containing textual information and links to MEDLINE
and sequence records in the Entrez system, and links
to additional related resources at NCBI and elsewhere.
In the HTML results page this ID links to the OMIM
page for that entry.
RefSeq_NCBI The Reference Sequence (RefSeq) identifier for that
entry, provided by the NCBI. As we do not aim to
curate all variants of a gene only one mapped RefSeq
is displayed per gene report. RefSeq aims to provide a
comprehensive, integrated, non-redundant set of
sequences, including genomic DNA, transcript (RNA),
and protein products. RefSeq identifiers are designed
to provide a stable reference for gene identification
and characterization, mutation analysis, expression
studies, polymorphism discovery, and comparative
analyses. In the HTML results page this ID links to
the RefSeq page for that entry.
UniProt_ID The UniProt identifier, provided by the EBI. The
UniProt Protein Knowledgebase is described as a
curated protein sequence database that provides a high
level of annotation, a minimal level of redundancy and
high level of integration with other databases. In the
HTML results page this ID links to the UniProt page
for that entry.
Ensembl_ID_Ensembl The Ensembl ID is derived from the current build of
the Ensembl database and provided by the Ensembl team.
UCSC_ID The UCSC ID is derived from the current build of the
UCSC database
Mouse_Genome_Database_ID_MGI MGI identifier. In the HTML results page this
ID links to the MGI Report for that gene.
Rat_Genome_Database_ID_RGD RGD identifier. In the HTML results page this ID
links to the RGD Report for that gene.