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

Gene ID: 2175, updated on 5-Mar-2024

Summary

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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
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Genomic context

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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

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Mutated FANCA Gene Role in the Modulation of Energy Metabolism and Mitochondrial Dynamics in Head and Neck Squamous Cell Carcinoma. Bertola N, et al. Cells, 2022 Jul 30. PMID 35954197, Free PMC Article
  2. Next-generation sequencing reveals novel variants and large deletion in FANCA gene in Polish family with Fanconi anemia. Repczynska A, et al. Orphanet J Rare Dis, 2022 Jul 19. PMID 35854323, Free PMC Article
  3. Esophageal cancer as initial presentation of Fanconi anemia in patients with a hypomorphic FANCA variant. Lach FP, et al. Cold Spring Harb Mol Case Stud, 2020 Dec. PMID 33172906, Free PMC Article
  4. Optimised molecular genetic diagnostics of Fanconi anaemia by whole exome sequencing and functional studies. Bogliolo M, et al. J Med Genet, 2020 Apr. PMID 31586946
  5. Rare variants in FANCA induce premature ovarian insufficiency. Yang X, et al. Hum Genet, 2019 Dec. PMID 31535215, Free PMC Article

See all (223) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. FANCA c.3624C>T (p.Ser1208=) is a hypomorphic splice variant associated with delayed onset of Fanconi anemia.
    Title: FANCA c.3624C>T (p.Ser1208=) is a hypomorphic splice variant associated with delayed onset of Fanconi anemia.
  2. BRCA-deficient metastatic prostate cancer has an adverse prognosis and distinct genomic phenotype.
    Title: BRCA-deficient metastatic prostate cancer has an adverse prognosis and distinct genomic phenotype.
  3. Mutated FANCA Gene Role in the Modulation of Energy Metabolism and Mitochondrial Dynamics in Head and Neck Squamous Cell Carcinoma.
    Title: Mutated FANCA Gene Role in the Modulation of Energy Metabolism and Mitochondrial Dynamics in Head and Neck Squamous Cell Carcinoma.
  4. Next-generation sequencing reveals novel variants and large deletion in FANCA gene in Polish family with Fanconi anemia.
    Title: Next-generation sequencing reveals novel variants and large deletion in FANCA gene in Polish family with Fanconi anemia.
  5. Fanconi anemia A protein participates in nucleolar homeostasis maintenance and ribosome biogenesis.
    Title: Fanconi anemia A protein participates in nucleolar homeostasis maintenance and ribosome biogenesis.
  6. SIK2 kinase synthetic lethality is driven by spindle assembly defects in FANCA-deficient cells.
    Title: SIK2 kinase synthetic lethality is driven by spindle assembly defects in FANCA-deficient cells.
  7. In silico study of missense variants of FANCA, FANCC and FANCG genes reveals high risk deleterious alleles predisposing to Fanconi anemia pathogenesis.
    Title: In silico study of missense variants of FANCA, FANCC and FANCG genes reveals high risk deleterious alleles predisposing to Fanconi anemia pathogenesis.
  8. Esophageal cancer as initial presentation of Fanconi anemia in patients with a hypomorphic FANCA variant.
    Title: Esophageal cancer as initial presentation of Fanconi anemia in patients with a hypomorphic FANCA variant.
  9. Clinical and Genetic Features of Patients With Fanconi Anemia in Lebanon and Report on Novel Mutations in the FANCA and FANCG Genes.
    Title: Clinical and Genetic Features of Patients With Fanconi Anemia in Lebanon and Report on Novel Mutations in the FANCA and FANCG Genes.
  10. Severe telomere shortening in Fanconi anemia complementation group L.
    Title: Severe telomere shortening in Fanconi anemia complementation group L.
Submit: New GeneRIF Correction See all GeneRIFs (71)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

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

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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)

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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_000135.4 → NP_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:1266 → 1312
    Fanconi_A; Fanconi anaemia group A protein
    pfam15865
    Location:172 → 522
    Fanconi_A_N; Fanconi anaemia group A protein N terminus

  2. NM_001018112.3 → NP_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:172 → 297
    Fanconi_A_N; Fanconi anaemia group A protein N terminus

  3. NM_001286167.3 → NP_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:1266 → 1312
    Fanconi_A; Fanconi anaemia group A protein
    pfam15865
    Location:172 → 522
    Fanconi_A_N; Fanconi anaemia group A protein N terminus

  4. NM_001351830.2 → NP_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:142 → 265
    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)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O15360.2 GenPept UniProtKB/Swiss-Prot:O15360

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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