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

Gene ID: 10144, updated on 2-Nov-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, Nov 2024]
Expression
Ubiquitous expression in fat (RPKM 21.4), thyroid (RPKM 14.6) and 25 other tissues See more
Orthologs
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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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