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    FAM13A family with sequence similarity 13 member A [ Homo sapiens (human) ]

    Gene ID: 10144, updated on 28-Oct-2024

    Summary

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    Official Symbol
    FAM13Aprovided by HGNC
    Official Full Name
    family with sequence similarity 13 member Aprovided by HGNC
    Primary source
    HGNC:HGNC:19367
    See related
    Ensembl:ENSG00000138640 MIM:613299; AllianceGenome:HGNC:19367
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    FAM13A1; ARHGAP48
    Summary
    Predicted to enable GTPase activator activity. Predicted to be involved in regulation of small GTPase mediated signal transduction. Predicted to be located in cytosol. Implicated in chronic obstructive pulmonary disease. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in fat (RPKM 21.4), thyroid (RPKM 14.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See FAM13A in Genome Data Viewer
    Location:
    4q22.1
    Exon count:
    32
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (88725960..89057185, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (92057646..92388672, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (89647111..89978336, complement)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene HECT and RLD domain containing E3 ubiquitin protein ligase 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21717 Neighboring gene RNA, U6 small nuclear 33, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:89642061-89642562 Neighboring gene FAM13A antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 7691 Neighboring gene nucleosome assembly protein 1 like 5 Neighboring gene HNF1 motif-containing MPRA enhancer 87 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:89743767-89744454 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:89744455-89745141 Neighboring gene uncharacterized LOC124900732 Neighboring gene uncharacterized LOC105377327 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:89908831-89909330 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr4:89928887-89930086 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:89977637-89978199 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21719 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21720 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21721 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21722 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15567 Neighboring gene RNA, U6 small nuclear 907, pseudogene Neighboring gene tigger transposable element derived 2

    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 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. Association of family sequence similarity gene 13A gene polymorphism and interstitial lung disease susceptibility: A systematic review and meta-analysis. Hu Y, et al. Mol Genet Genomic Med, 2023 Nov. PMID 37786320, Free PMC Article
    2. Identification of FAM13A gene associated with the ratio of FEV1 to FVC in Korean population by genome-wide association studies including gene-environment interactions. Kim S, et al. J Hum Genet, 2015 Mar. PMID 25608829
    3. Moving beyond genetics: is FAM13A a major biological contributor in lung physiology and chronic lung diseases? Corvol H, et al. J Med Genet, 2014 Oct. PMID 25163686
    4. FAM13A polymorphism as a prognostic factor in patients with idiopathic pulmonary fibrosis. Hirano C, et al. Respir Med, 2017 Feb. PMID 28137485
    5. Quantitative analysis of lungs and airways with CT in subjects with the chronic obstructive pulmonary disease (COPD) candidate FAM13A gene: case control study for CT quantification in COPD risk gene. Choo JY, et al. J Comput Assist Tomogr, 2014 Jul-Aug. PMID 24651745

    See all (70) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The FAM13A Long Isoform Regulates Cilia Movement and Coordination in Airway Mucociliary Transport.
      Title: The FAM13A Long Isoform Regulates Cilia Movement and Coordination in Airway Mucociliary Transport.
    2. Association of family sequence similarity gene 13A gene polymorphism and interstitial lung disease susceptibility: A systematic review and meta-analysis.
      Title: Association of family sequence similarity gene 13A gene polymorphism and interstitial lung disease susceptibility: A systematic review and meta-analysis.
    3. FAM13A regulates cellular senescence marker p21 and mitochondrial reactive oxygen species production in airway epithelial cells.
      Title: FAM13A regulates cellular senescence marker p21 and mitochondrial reactive oxygen species production in airway epithelial cells.
    4. FAM13A polymorphisms are associated with a specific susceptibility to clinical progression of oral cancer in alcohol drinkers.
      Title: FAM13A polymorphisms are associated with a specific susceptibility to clinical progression of oral cancer in alcohol drinkers.
    5. Single Nucleotide Polymorphisms of FAM13A Gene in Chronic Obstructive Pulmonary Disease-A Case Control Study in Vietnam.
      Title: Single Nucleotide Polymorphisms of FAM13A Gene in Chronic Obstructive Pulmonary Disease-A Case Control Study in Vietnam.
    6. The Influence of FAM13A and PPAR-gamma2 Gene Polymorphisms on the Metabolic State of Postmenopausal Women.
      Title: The Influence of FAM13A and PPAR-γ2 Gene Polymorphisms on the Metabolic State of Postmenopausal Women.
    7. Association of a FAM13A variant with interstitial lung disease in Japanese rheumatoid arthritis.
      Title: Association of a FAM13A variant with interstitial lung disease in Japanese rheumatoid arthritis.
    8. miR30a5p induces the adipogenic differentiation of bone marrow mesenchymal stem cells by targeting FAM13A/Wnt/betacatenin signaling in aplastic anemia.
      Title: miR‑30a‑5p induces the adipogenic differentiation of bone marrow mesenchymal stem cells by targeting FAM13A/Wnt/β‑catenin signaling in aplastic anemia.
    9. Family with sequence similarity 13 member A mediates TGF-beta1-induced EMT in small airway epithelium of patients with chronic obstructive pulmonary disease.
      Title: Family with sequence similarity 13 member A mediates TGF-β1-induced EMT in small airway epithelium of patients with chronic obstructive pulmonary disease.
    10. Connecting COPD GWAS Genes: FAM13A Controls TGFbeta2 Secretion by Modulating AP-3 Transport.
      Title: Connecting COPD GWAS Genes: FAM13A Controls TGFβ2 Secretion by Modulating AP-3 Transport.
    Submit: New GeneRIF Correction See all GeneRIFs (41)

    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

    EBI GWAS Catalog

    Description
    A genome-wide association study of COPD identifies a susceptibility locus on chromosome 19q13.
    EBI GWAS Catalog
    Discovery and refinement of loci associated with lipid levels.
    EBI GWAS Catalog
    Genetic susceptibility for chronic bronchitis in chronic obstructive pulmonary disease.
    EBI GWAS Catalog
    Genome-wide association study identifies multiple susceptibility loci for pulmonary fibrosis.
    EBI GWAS Catalog
    Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function.
    EBI GWAS Catalog
    Genomewide association study of movement-related adverse antipsychotic effects.
    EBI GWAS Catalog
    IREB2 and GALC are Associated with Pulmonary Artery Enlargement in Chronic Obstructive Pulmonary Disease.
    EBI GWAS Catalog
    Meta-analyses of genome-wide association studies identify multiple loci associated with pulmonary function.
    EBI GWAS Catalog
    Risk loci for chronic obstructive pulmonary disease: a genome-wide association study and meta-analysis.
    EBI GWAS Catalog
    Variants in FAM13A are associated with chronic obstructive pulmonary disease.
    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

    • FLJ34562, MGC105131

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables GTPase activator activity TAS
    Traceable Author Statement
    more info
    		  
    Process Evidence Code Pubs
    involved_in regulation of small GTPase mediated signal transduction TAS
    Traceable Author Statement
    more info
    		  
    involved_in signal transduction IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    protein FAM13A
    Names
    FAM13A1_v2 protein
    family with sequence similarity 13, member A1

    NCBI Reference Sequences (RefSeq)

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    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.

    mRNA and Protein(s)

    1. NM_001015045.3 → NP_001015045.1  protein FAM13A isoform b

      See identical proteins and their annotated locations for NP_001015045.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (b) is shorter and has a distinct N-terminus, compared to isoform a.
      Source sequence(s)
      AK027138, BC053569, BN000265, DA450095
      Consensus CDS
      CCDS43251.1
      UniProtKB/Swiss-Prot
      O94988
      Related
      ENSP00000421562.1, ENST00000508369.5

    2. NM_001265578.2 → NP_001252507.1  protein FAM13A isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and has multiple differences in the coding region, including the use of an alternate start codon, compared to variant 1. The encoded isoform (c) is shorter and has a distinct N-terminus, compared to isoform a.
      Source sequence(s)
      BC086875, BN000265, DA450095
      Consensus CDS
      CCDS58912.1
      UniProtKB/Swiss-Prot
      O94988
      Related
      ENSP00000427189.1, ENST00000503556.5

    3. NM_001265579.2 → NP_001252508.1  protein FAM13A isoform d

      See identical proteins and their annotated locations for NP_001252508.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and has multiple differences in the coding region, including the use of an alternate start codon, compared to variant 1. The encoded isoform (d) is shorter and has a distinct N-terminus, compared to isoform a.
      Source sequence(s)
      AB020721, BN000265, DA450095
      Consensus CDS
      CCDS58913.1
      UniProtKB/Swiss-Prot
      O94988
      Related
      ENSP00000378450.2, ENST00000395002.6

    4. NM_001265580.2 → NP_001252509.1  protein FAM13A isoform e

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR and has multiple differences in the coding region, including the use of an alternate start codon, compared to variant 1. The encoded isoform (e) is shorter and has a distinct N-terminus, compared to isoform a.
      Source sequence(s)
      AK296932, BN000265, DA450095
      Consensus CDS
      CCDS58911.1
      UniProtKB/TrEMBL
      E9PGM7
      Related
      ENSP00000423252.1, ENST00000513837.5

    5. NM_014883.4 → NP_055698.2  protein FAM13A isoform a

      See identical proteins and their annotated locations for NP_055698.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      BN000265, DA692373
      Consensus CDS
      CCDS34029.1
      UniProtKB/Swiss-Prot
      B4DLC1, O94988, Q24JP0, Q5PR21, Q8NBA3
      UniProtKB/TrEMBL
      A0A2X0SFT1
      Related
      ENSP00000264344.5, ENST00000264344.10
      Conserved Domains (2) summary
      cd04393
      Location:39 → 226
      RhoGAP_FAM13A1a; RhoGAP_FAM13A1a: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of FAM13A1, isoform a-like proteins. The function of FAM13A1a is unknown. Small GTPases cluster into distinct families, and all act as molecular switches, active ...
      pfam15905
      Location:617 → 819
      HMMR_N; Hyaluronan mediated motility receptor N-terminal

    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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      88725960..89057185 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047449481.1 → XP_047305437.1  protein FAM13A isoform X8

    2. XM_047449479.1 → XP_047305435.1  protein FAM13A isoform X2

    3. XM_011531516.2 → XP_011529818.1  protein FAM13A isoform X1

      See identical proteins and their annotated locations for XP_011529818.1

      UniProtKB/Swiss-Prot
      B4DLC1, O94988, Q24JP0, Q5PR21, Q8NBA3
      UniProtKB/TrEMBL
      A0A2X0SFT1
      Conserved Domains (2) summary
      cd04393
      Location:39 → 226
      RhoGAP_FAM13A1a; RhoGAP_FAM13A1a: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of FAM13A1, isoform a-like proteins. The function of FAM13A1a is unknown. Small GTPases cluster into distinct families, and all act as molecular switches, active ...
      pfam15905
      Location:617 → 819
      HMMR_N; Hyaluronan mediated motility receptor N-terminal

    4. XM_047449482.1 → XP_047305438.1  protein FAM13A isoform X9

    5. XM_047449480.1 → XP_047305436.1  protein FAM13A isoform X6

    6. XM_011531517.3 → XP_011529819.1  protein FAM13A isoform X3

      UniProtKB/TrEMBL
      A0A2X0SFT1
      Conserved Domains (2) summary
      cd04393
      Location:39 → 226
      RhoGAP_FAM13A1a; RhoGAP_FAM13A1a: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of FAM13A1, isoform a-like proteins. The function of FAM13A1a is unknown. Small GTPases cluster into distinct families, and all act as molecular switches, active ...
      pfam15905
      Location:589 → 791
      HMMR_N; Hyaluronan mediated motility receptor N-terminal

    7. XM_017007624.3 → XP_016863113.1  protein FAM13A isoform X5

      UniProtKB/TrEMBL
      A0A2X0SFT1

    8. XM_005262683.4 → XP_005262740.1  protein FAM13A isoform X4

      UniProtKB/TrEMBL
      A0A2X0SFT1
      Conserved Domains (2) summary
      cd04393
      Location:39 → 226
      RhoGAP_FAM13A1a; RhoGAP_FAM13A1a: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of FAM13A1, isoform a-like proteins. The function of FAM13A1a is unknown. Small GTPases cluster into distinct families, and all act as molecular switches, active ...
      pfam15905
      Location:617 → 819
      HMMR_N; Hyaluronan mediated motility receptor N-terminal

    9. XM_017007625.1 → XP_016863114.1  protein FAM13A isoform X7

      UniProtKB/TrEMBL
      A0A2X0SFT1

    10. XM_011531518.2 → XP_011529820.1  protein FAM13A isoform X11

      See identical proteins and their annotated locations for XP_011529820.1

      UniProtKB/TrEMBL
      A0A2X0SFT1
      Conserved Domains (2) summary
      pfam15905
      Location:431 → 633
      HMMR_N; Hyaluronan mediated motility receptor N-terminal
      cl02570
      Location:1 → 40
      RhoGAP; RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when ...

    11. XM_017007626.1 → XP_016863115.1  protein FAM13A isoform X10

      UniProtKB/TrEMBL
      A0A2X0SFT1

    12. XM_047449483.1 → XP_047305439.1  protein FAM13A isoform X11

    13. XM_011531519.4 → XP_011529821.1  protein FAM13A isoform X11

      See identical proteins and their annotated locations for XP_011529821.1

      UniProtKB/TrEMBL
      A0A2X0SFT1
      Conserved Domains (2) summary
      pfam15905
      Location:431 → 633
      HMMR_N; Hyaluronan mediated motility receptor N-terminal
      cl02570
      Location:1 → 40
      RhoGAP; RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when ...

    14. XM_047449485.1 → XP_047305441.1  protein FAM13A isoform X13

    15. XM_006714057.4 → XP_006714120.1  protein FAM13A isoform X12

      UniProtKB/TrEMBL
      A0A2X0SFT1
      Conserved Domains (1) summary
      cl02570
      Location:10 → 37
      RhoGAP; RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when ...

    16. XM_017007633.3 → XP_016863122.1  protein FAM13A isoform X14

    17. XM_047449484.1 → XP_047305440.1  protein FAM13A isoform X13

    18. XM_047449487.1 → XP_047305443.1  protein FAM13A isoform X16

    19. XM_017007634.3 → XP_016863123.1  protein FAM13A isoform X15

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      92057646..92388672 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054348707.1 → XP_054204682.1  protein FAM13A isoform X8

    2. XM_054348700.1 → XP_054204675.1  protein FAM13A isoform X2

    3. XM_054348698.1 → XP_054204673.1  protein FAM13A isoform X1

      UniProtKB/Swiss-Prot
      B4DLC1, O94988, Q24JP0, Q5PR21, Q8NBA3

    4. XM_054348708.1 → XP_054204683.1  protein FAM13A isoform X9

    5. XM_054348704.1 → XP_054204679.1  protein FAM13A isoform X6

    6. XM_054348706.1 → XP_054204681.1  protein FAM13A isoform X8

    7. XM_054348701.1 → XP_054204676.1  protein FAM13A isoform X3

    8. XM_054348703.1 → XP_054204678.1  protein FAM13A isoform X5

    9. XM_054348699.1 → XP_054204674.1  protein FAM13A isoform X2

    10. XM_054348702.1 → XP_054204677.1  protein FAM13A isoform X4

    11. XM_054348705.1 → XP_054204680.1  protein FAM13A isoform X7

    12. XM_054348711.1 → XP_054204686.1  protein FAM13A isoform X11

    13. XM_054348709.1 → XP_054204684.1  protein FAM13A isoform X10

    14. XM_054348710.1 → XP_054204685.1  protein FAM13A isoform X11

    15. XM_054348714.1 → XP_054204689.1  protein FAM13A isoform X13

    16. XM_054348712.1 → XP_054204687.1  protein FAM13A isoform X12

    17. XM_054348713.1 → XP_054204688.1  protein FAM13A isoform X13

    18. XM_054348716.1 → XP_054204691.1  protein FAM13A isoform X16

    19. XM_054348715.1 → XP_054204690.1  protein FAM13A isoform X15

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O94988.2 GenPept UniProtKB/Swiss-Prot:O94988

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