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FANCA FA complementation group A [ Homo sapiens (human) ]

Gene ID: 2175, updated on 5-Jul-2020

Summary

Official Symbol
FANCAprovided by HGNC
Official Full Name
FA complementation group Aprovided by HGNC
Primary source
HGNC:HGNC:3582
See related
Ensembl:ENSG00000187741 MIM:607139
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
FA; FA1; FAA; FAH; FA-H; FACA; FANCH
Summary
The Fanconi anemia complementation group (FANC) currently includes FANCA, FANCB, FANCC, FANCD1 (also called BRCA2), FANCD2, FANCE, FANCF, FANCG, FANCI, FANCJ (also called BRIP1), FANCL, FANCM and FANCN (also called PALB2). The previously defined group FANCH is the same as FANCA. Fanconi anemia is a genetically heterogeneous recessive disorder characterized by cytogenetic instability, hypersensitivity to DNA crosslinking agents, increased chromosomal breakage, and defective DNA repair. The members of the Fanconi anemia complementation group do not share sequence similarity; they are related by their assembly into a common nuclear protein complex. This gene encodes the protein for complementation group A. Alternative splicing results in multiple transcript variants encoding different isoforms. Mutations in this gene are the most common cause of Fanconi anemia. [provided by RefSeq, Jul 2008]
Expression
Broad expression in lymph node (RPKM 7.2), bone marrow (RPKM 6.7) and 25 other tissues See more
Orthologs

Genomic context

See FANCA in Genome Data Viewer
Location:
16q24.3
Exon count:
44
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 16 NC_000016.10 (89737549..89816647, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (89803959..89883066, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene spermatogenesis associated 2 like Neighboring gene VPS9D1 antisense RNA 1 Neighboring gene VPS9 domain containing 1 Neighboring gene zinc finger protein 276 Neighboring gene Sharpr-MPRA regulatory region 3988 Neighboring gene uncharacterized LOC107984817 Neighboring gene spire type actin nucleation factor 2 Neighboring gene uncharacterized LOC105371419

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Common genetic loci influencing plasma homocysteine concentrations and their effect on risk of coronary artery disease.
NHGRI GWA Catalog
Genome-wide association analyses identify 13 new susceptibility loci for generalized vitiligo.
NHGRI GWA Catalog
Genome-wide meta-analysis identifies regions on 7p21 (AHR) and 15q24 (CYP1A2) as determinants of habitual caffeine consumption.
NHGRI GWA Catalog
Web-based, participant-driven studies yield novel genetic associations for common traits.
NHGRI GWA Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC75158

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
DNA repair TAS
Traceable Author Statement
more info
 
female gonad development IEA
Inferred from Electronic Annotation
more info
 
interstrand cross-link repair TAS
Traceable Author Statement
more info
 
male gonad development IEA
Inferred from Electronic Annotation
more info
 
male meiotic nuclear division IEA
Inferred from Electronic Annotation
more info
 
protein-containing complex assembly TAS
Traceable Author Statement
more info
PubMed 
regulation of CD40 signaling pathway IEA
Inferred from Electronic Annotation
more info
 
regulation of DNA-binding transcription factor activity IEA
Inferred from Electronic Annotation
more info
 
regulation of cell proliferation IEA
Inferred from Electronic Annotation
more info
 
regulation of inflammatory response IEA
Inferred from Electronic Annotation
more info
 
regulation of regulatory T cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
Fanconi anaemia nuclear complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Fanconi anaemia nuclear complex IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
Fanconi anemia group A protein
Names
Fanconi anemia complementation group A
Fanconi anemia, complementation group H
Fanconi anemia, type 1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_011706.1 RefSeqGene

    Range
    5001..84107
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_495

mRNA and Protein(s)

  1. NM_000135.4NP_000126.2  Fanconi anemia group A protein isoform a

    See identical proteins and their annotated locations for NP_000126.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AC005360, AC005567, BC064540, X99226
    Consensus CDS
    CCDS32515.1
    UniProtKB/Swiss-Prot
    O15360
    Related
    ENSP00000373952.3, ENST00000389301.8
    Conserved Domains (2) summary
    pfam03511
    Location:12661312
    Fanconi_A; Fanconi anaemia group A protein
    pfam15865
    Location:172522
    Fanconi_A_N; Fanconi anaemia group A protein N terminus
  2. NM_001018112.3NP_001018122.1  Fanconi anemia group A protein isoform b

    See identical proteins and their annotated locations for NP_001018122.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate exon, which results in an early stop codon, compared to variant 1. The resulting protein (isoform b) has a shorter C-terminus, compared to isoform a.
    Source sequence(s)
    AC005567, BC008979, BY995664
    Consensus CDS
    CCDS42221.1
    UniProtKB/Swiss-Prot
    O15360
    Related
    ENSP00000373953.3, ENST00000389302.7
    Conserved Domains (1) summary
    pfam15865
    Location:172297
    Fanconi_A_N; Fanconi anaemia group A protein N terminus
  3. NM_001286167.3NP_001273096.1  Fanconi anemia group A protein isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate splice junction in a 3' coding exon compared to variant 1, that causes a frameshift. The resulting isoform (c) has a shorter and distinct C-terminus compared to isoform a.
    Source sequence(s)
    AC005360, AK299282, BC064540, X99226
    Consensus CDS
    CCDS67099.1
    UniProtKB/Swiss-Prot
    O15360
    Related
    ENSP00000456829.1, ENST00000568369.5
    Conserved Domains (2) summary
    pfam03511
    Location:12661312
    Fanconi_A; Fanconi anaemia group A protein
    pfam15865
    Location:172522
    Fanconi_A_N; Fanconi anaemia group A protein N terminus
  4. NM_001351830.2NP_001338759.1  Fanconi anemia group A protein isoform d

    Status: REVIEWED

    Source sequence(s)
    AC005567, BC008979, BC120978, BY995664
    Consensus CDS
    CCDS86554.1
    Related
    ENSP00000443409.1, ENST00000543736.5
    Conserved Domains (1) summary
    pfam15865
    Location:142265
    Fanconi_A_N; Fanconi anaemia group A protein N terminus

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p13 Primary Assembly

    Range
    89737549..89816647 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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