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

    Gene ID: 2175, updated on 27-Nov-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
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (89737549..89816647, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (95822301..95901198, complement)
    RS_2024_09 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. Unusual splice site mutations disrupt FANCA exon 8 definition. Mattioli C, et al. Biochim Biophys Acta, 2014 Jul. PMID 24704046
    2. Comprehensive association testing of common genetic variation in DNA repair pathway genes in relationship with breast cancer risk in multiple populations. Haiman CA, et al. Hum Mol Genet, 2008 Mar 15. PMID 18056155
    3. [Construction of FANCA mutant protein from Fanconi anemia patient and analysis of its function]. Chen F, et al. Zhonghua Xue Ye Xue Za Zhi, 2007 Nov. PMID 18457264
    4. Fanconi anemia deficiency stimulates HPV-associated hyperplastic growth in organotypic epithelial raft culture. Hoskins EE, et al. Oncogene, 2009 Feb 5. PMID 19015634, Free PMC Article
    5. Fanca-/- hematopoietic stem cells demonstrate a mobilization defect which can be overcome by administration of the Rac inhibitor NSC23766. Milsom MD, et al. Haematologica, 2009 Jul. PMID 19491337, Free PMC Article

    See all (233) 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)

    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 
    located_in 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_2024_08

    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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