HGNC data archive help
The HGNC now archive the complete HGNC dataset file (both tab separated and JSON formats) for each month and each quarter and store them in our Google Cloud Storage Bucket.
File fields/columns information
The monthly files are produced on the 1st of every month while the quarterly files are produced on the 1st of Jan, Apr, Jul & Oct. If a monthly file is over 365 days old, the file will be deleted for us to save disk space however, the quarterly files are not deleted currently so for snapshots older than 365 days please use the quarterly files.
There are essentially two types of data file (excluding the file format type) of hgnc_complete_set and withdraw. The hgnc_complete_set is a set of all approved gene symbol reports found on the GRCh38 reference and the alternative reference loci (see fig. 1 for a list of columns/headings).
hgnc_id = HGNC ID. A unique ID created by the HGNC for every
approved symbol.
symbol = The HGNC approved gene symbol. Equates to the
"APPROVED SYMBOL" field within the gene symbol
report.
name = HGNC approved name for the gene. Equates to the
"APPROVED NAME" field within the gene symbol report.
locus_group = A group name for a set of related locus types as
defined by the HGNC (e.g. non-coding RNA).
locus_type = The locus type as defined by the HGNC (e.g. RNA,
transfer).
status = Status of the symbol report, which can be either
"Approved" or "Entry Withdrawn".
location = Cytogenetic location of the gene (e.g. 2q34).
location_sortable = Same as "location" but single digit chromosomes are
prefixed with a 0 enabling them to be sorted in
correct numerical order (e.g. 02q34).
alias_symbol = Other symbols used to refer to this gene as seen in
the "SYNONYMS" field in the symbol report.
alias_name = Other names used to refer to this gene as seen in
the "SYNONYMS" field in the gene symbol report.
prev_symbol = Symbols previously approved by the HGNC for this
gene. Equates to the "PREVIOUS SYMBOLS & NAMES" field
within the gene symbol report.
prev_name = Gene names previously approved by the HGNC for this
gene. Equates to the "PREVIOUS SYMBOLS & NAMES" field
within the gene symbol report.
gene_family = Name given to a gene family or group the gene has been
assigned to. Equates to the "GENE FAMILY" field within
the gene symbol report.
gene_family_id = ID used to designate a gene family or group the gene
has been assigned to.
date_approved_reserved = The date the entry was first approved.
date_symbol_changed = The date the gene symbol was last changed.
date_name_changed = The date the gene name was last changed.
date_modified = Date the entry was last modified.
entrez_id = Entrez gene ID. Found within the "GENE RESOURCES"
section of the gene symbol report.
ensembl_gene_id = Ensembl gene ID. Found within the "GENE RESOURCES"
section of the gene symbol report.
vega_id = Vega gene ID. Found within the "GENE RESOURCES"
section of the gene symbol report.
ucsc_id = UCSC gene ID. Found within the "GENE RESOURCES"
section of the gene symbol report.
ena = International Nucleotide Sequence Database
Collaboration (GenBank, ENA and DDBJ) accession
number(s). Found within the "NUCLEOTIDE SEQUENCES"
section of the gene symbol report.
refseq_accession = RefSeq nucleotide accession(s). Found within the
"NUCLEOTIDE SEQUENCES" section of the gene symbol
report.
ccds_id = Consensus CDS ID. Found within the
"NUCLEOTIDE SEQUENCES" section of the gene symbol
report.
uniprot_ids = UniProt protein accession. Found within the
"PROTEIN RESOURCES" section of the gene symbol
report.
pubmed_id = Pubmed and Europe Pubmed Central PMID(s).
mgd_id = Mouse genome informatics database ID. Found within
the "HOMOLOGS" section of the gene symbol report.
rgd_id = Rat genome database gene ID. Found within the
"HOMOLOGS" section of the gene symbol report.
lsdb = The name of the Locus Specific Mutation Database and
URL for the gene separated by a | character
cosmic = Symbol used within the Catalogue of somatic
mutations in cancer for the gene.
omim_id = Online Mendelian Inheritance in Man (OMIM) ID
mirbase = miRBase ID
homeodb = Homeobox Database ID
snornabase = snoRNABase ID
bioparadigms_slc = Symbol used to link to the SLC tables database at
bioparadigms.org for the gene
orphanet = Orphanet ID
pseudogene.org = Pseudogene.org
horde_id = Symbol used within HORDE for the gene
merops = ID used to link to the MEROPS peptidase database
imgt = Symbol used within international ImMunoGeneTics
information system
iuphar = The objectId used to link to the IUPHAR/BPS Guide to
PHARMACOLOGY database. To link to IUPHAR/BPS Guide
to PHARMACOLOGY database only use the number
(only use 1 from the result objectId:1)
kznf_gene_catalog = ID used to link to the Human KZNF Gene Catalog
mamit-trnadb = ID to link to the Mamit-tRNA database
cd = Symbol used within the Human Cell Differentiation
Molecule database for the gene
lncrnadb = lncRNA Database ID - Resource now defunct
enzyme_id = ENZYME EC accession number
intermediate_filament_db = ID used to link to the Human Intermediate Filament
Database
agr = The HGNC ID that the Alliance of Genome Resources
(AGR) have linked to their record of the gene. Use
the HGNC ID to link to the AGR.
mane_select = NCBI and Ensembl transcript IDs/acessions
including the version number for one high-quality
representative transcript per protein-coding gene
that is well-supported by experimental data and
represents the biology of the gene. The IDs are
delimited by |.
The withdrawn file contains all gene symbol reports that are no longer approved. Either the symbol has been withdrawn or merged/split into another report (see fig. 2 for a list of columns/headings).
HGNC_ID = The HGNC ID of the withdrawn record.
STATUS = Can either be "Entry Withdrawn" or "Merged/Split"
WITHDRAWN_SYMBOL = The symbol of the withdrawn record.
MERGED_INTO_REPORT(S) = Shows what record(s) replaced the withdrawn record if the
status is "Merged/Split". Each replacement has the format
HGNC_ID|SYMBOL|STATUS. If the withdrawn record is split,
their will be more than one replacement and they will be
comma separated.
Archive files location
- Monthly files:
- Quarterly files: