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

    Gene ID: 2175, updated on 17-Jun-2024

    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; AllianceGenome:HGNC:3582
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See FANCA in Genome Data Viewer
    Location:
    16q24.3
    Exon count:
    44
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (89737549..89816647, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (95822301..95901198, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (89803957..89883055, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:89765851-89766716 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7920 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7921 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11418 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:89772795-89773295 Neighboring gene spermatogenesis associated 2 like Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:89777095-89777658 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7922 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11419 Neighboring gene VPS9D1 antisense RNA 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46687 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7923 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7924 Neighboring gene VPS9 domain containing 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:89795065-89795636 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46690 Neighboring gene zinc finger protein 276 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46704 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46706 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46707/46708 Neighboring gene MPRA-validated peak2667 silencer Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46713 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46714 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46718 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11420 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11421 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr16:89846248-89846785 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:89872952-89873474 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7925 Neighboring gene Sharpr-MPRA regulatory region 3988 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11422 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46779 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7927 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:89900233-89901432 Neighboring gene uncharacterized LOC124903760 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:89903444-89904066 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:89904067-89904688 Neighboring gene spire type actin nucleation factor 2 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:89913406 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:89913685-89914304 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:89914305-89914923 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:89920364-89920864 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:89920865-89921365 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11423 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11424 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11425 Neighboring gene uncharacterized LOC112268179 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:89938758-89939714 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7928

    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

    Associated conditions

    Description Tests
    Fanconi anemia complementation group A
    MedGen: C3469521 OMIM: 227650 GeneReviews: Fanconi Anemia
    Compare labs

    EBI GWAS Catalog

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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC75158

    Gene Ontology Provided by GOA

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

    NEW Try the new Transcript table

    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
      A5D923, B4DRI7, H3BSR5, O15360, O75266, Q6PL10, Q92497, Q96H18, Q9UEA5, Q9UEL8, Q9UEL9, Q9UPK3, Q9Y6M2
      UniProtKB/TrEMBL
      H3BNS0
      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/TrEMBL
      A0PJU8, Q86U55
      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/TrEMBL
      H3BNS0
      Related
      ENSP00000456829.1, ENST00000568369.6
      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
      UniProtKB/TrEMBL
      A0PJU8, Q0VAP4
      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: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

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

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      95822301..95901198 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)