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    FOCAD focadhesin [ Homo sapiens (human) ]

    Gene ID: 54914, updated on 5-Mar-2024

    Summary

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    Official Symbol
    FOCADprovided by HGNC
    Official Full Name
    focadhesinprovided by HGNC
    Primary source
    HGNC:HGNC:23377
    See related
    Ensembl:ENSG00000188352 MIM:614606; AllianceGenome:HGNC:23377
    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
    SCOLIV; KIAA1797
    Summary
    Located in focal adhesion. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in thyroid (RPKM 11.9), adrenal (RPKM 7.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    9p21.3
    Exon count:
    49
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (20655625..20995950)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (20669421..21009826)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (20658308..20995949)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene MLLT3 super elongation complex subunit Neighboring gene microRNA 4474 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28227 Neighboring gene ribosomal protein L7a pseudogene 48 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28228 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19796 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19797 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28229 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19798 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19799 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19801 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19800 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28230 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:20683960-20684700 Neighboring gene FOCAD antisense RNA 1 Neighboring gene microRNA 491 Neighboring gene small nucleolar RNA, H/ACA box 30B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19803 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:21031418-21031978 Neighboring gene uncharacterized LOC105375989 Neighboring gene 3-hydroxyacyl-CoA dehydratase 4

    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. FOCAD Indel in a Family With Juvenile Polyposis Syndrome. MacFarland SP, et al. J Pediatr Gastroenterol Nutr, 2022 Jul 1. PMID 35622075
    2. Germline deletions in the tumour suppressor gene FOCAD are associated with polyposis and colorectal cancer development. Weren RD, et al. J Pathol, 2015 Jun. PMID 25712196, Free PMC Article
    3. Inter-tissue coexpression network analysis reveals DPP4 as an important gene in heart to blood communication. Long Q, et al. Genome Med, 2016 Feb 9. PMID 26856537, Free PMC Article
    4. Bivariate genetic association of KIAA1797 with heart rate in American Indians: the Strong Heart Family Study. Melton PE, et al. Hum Mol Genet, 2010 Sep 15. PMID 20601674, Free PMC Article
    5. KIAA1797/FOCAD encodes a novel focal adhesion protein with tumour suppressor function in gliomas. Brockschmidt A, et al. Brain, 2012 Apr. PMID 22427331

    See all (32) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Loss of FOCAD, operating via the SKI messenger RNA surveillance pathway, causes a pediatric syndrome with liver cirrhosis.
      Title: Loss of FOCAD, operating via the SKI messenger RNA surveillance pathway, causes a pediatric syndrome with liver cirrhosis.
    2. FOCAD Indel in a Family With Juvenile Polyposis Syndrome.
      Title: FOCAD Indel in a Family With Juvenile Polyposis Syndrome.
    3. FOCAD loss impacts microtubule assembly, G2/M progression and patient survival in astrocytic gliomas.
      Title: FOCAD loss impacts microtubule assembly, G2/M progression and patient survival in astrocytic gliomas.
    4. Results identified cardiac FOCAD expression to be correlated with protein biosynthetic processes in the lung. mediator of this process between the heart and lung.
      Title: Inter-tissue coexpression network analysis reveals DPP4 as an important gene in heart to blood communication.
    5. The data suggests that nonallelic germline deletions in the tumor suppressor gene FOCAD underlie moderate genetic predisposition to the development of polyposis and CRC
      Title: Germline deletions in the tumour suppressor gene FOCAD are associated with polyposis and colorectal cancer development.
    6. This stduy showed that frequently deleted KIAA1797 gene encodes a novel focal adhesion complex protein with tumour suppressor function in gliomas.
      Title: KIAA1797/FOCAD encodes a novel focal adhesion protein with tumour suppressor function in gliomas.
    7. KIAA1797 genetic variation is associated with heart rate.
      Title: Bivariate genetic association of KIAA1797 with heart rate in American Indians: the Strong Heart Family Study.
    8. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    9. Observational study of gene-disease association. (HuGE Navigator)
      Title: Bivariate genetic association of KIAA1797 with heart rate in American Indians: the Strong Heart Family Study.
    Submit: New GeneRIF Correction

    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
    Liver disease, severe congenital
    MedGen: C5774195 OMIM: 619991 GeneReviews: Not available
    		not available

    EBI GWAS Catalog

    Description
    Meta-analysis of genome-wide association studies in multiethnic Asians identifies two loci for age-related nuclear cataract.
    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

    • FLJ20375, KIAA1797

    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 regulation of post-transcriptional gene silencing IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in focal adhesion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    focadhesin

    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_001375567.1 → NP_001362496.1  focadhesin isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same isoform (1).
      Source sequence(s)
      AL354879, AL392163, AL445624, AL662879, KF458909
      Consensus CDS
      CCDS34993.1
      UniProtKB/Swiss-Prot
      D3DRJ9, Q5VW36, Q6ZME1, Q8IZG0, Q96JM8, Q96MS9, Q9BVF3, Q9NX87
      Related
      ENSP00000344307.6, ENST00000338382.11
      Conserved Domains (2) summary
      pfam11229
      Location:1213 → 1801
      Focadhesin
      pfam12530
      Location:490 → 714
      DUF3730; Protein of unknown function (DUF3730)

    2. NM_001375568.1 → NP_001362497.1  focadhesin isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an in-frame coding exon in the mid-coding region compared to variant 1, resulting in a shorter isoform (2) lacking an internal protein segment compared to isoform 1. Note, while isoforms 2 and 3 are the same length (1766 aa), they lack different protein segments compared to isoform 1.
      Source sequence(s)
      AL354879, AL392163, AL445624, AL662879, KF458909
      Conserved Domains (2) summary
      pfam11229
      Location:1178 → 1766
      Focadhesin
      pfam12530
      Location:453 → 679
      DUF3730; Protein of unknown function (DUF3730)

    3. NM_001375570.1 → NP_001362499.1  focadhesin isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks an in-frame coding exon in the 5'-coding region compared to variant 1, resulting in a shorter isoform (3) lacking an internal protein segment compared to isoform 1. Note, while isoforms 2 and 3 are the same length (1766 aa), they lack different protein segments compared to isoform 1.
      Source sequence(s)
      AL354879, AL392163, AL445624, AL662879, KF458909
      Conserved Domains (2) summary
      pfam11229
      Location:1178 → 1766
      Focadhesin
      pfam12530
      Location:455 → 679
      DUF3730; Protein of unknown function (DUF3730)

    4. NM_017794.5 → NP_060264.4  focadhesin isoform 1

      See identical proteins and their annotated locations for NP_060264.4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1). Variants 1 and 2 encode the same isoform.
      Source sequence(s)
      AK055116, AK056522, AL445624, AY139834
      Consensus CDS
      CCDS34993.1
      UniProtKB/Swiss-Prot
      D3DRJ9, Q5VW36, Q6ZME1, Q8IZG0, Q96JM8, Q96MS9, Q9BVF3, Q9NX87
      Related
      ENSP00000369599.1, ENST00000380249.5
      Conserved Domains (2) summary
      pfam11229
      Location:1213 → 1801
      Focadhesin
      pfam12530
      Location:490 → 714
      DUF3730; Protein of unknown function (DUF3730)

    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_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      20655625..20995950
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047423537.1 → XP_047279493.1  focadhesin isoform X4

      UniProtKB/Swiss-Prot
      D3DRJ9, Q5VW36, Q6ZME1, Q8IZG0, Q96JM8, Q96MS9, Q9BVF3, Q9NX87

    2. XM_047423539.1 → XP_047279495.1  focadhesin isoform X2

    3. XM_017014855.2 → XP_016870344.1  focadhesin isoform X11

    4. XM_047423532.1 → XP_047279488.1  focadhesin isoform X10

    5. XM_047423535.1 → XP_047279491.1  focadhesin isoform X13

    6. XM_047423534.1 → XP_047279490.1  focadhesin isoform X12

    7. XM_017014852.2 → XP_016870341.2  focadhesin isoform X8

    8. XM_047423533.1 → XP_047279489.1  focadhesin isoform X1

    9. XM_047423536.1 → XP_047279492.1  focadhesin isoform X3

    10. XM_047423531.1 → XP_047279487.1  focadhesin isoform X9

    11. XM_047423538.1 → XP_047279494.1  focadhesin isoform X4

      UniProtKB/Swiss-Prot
      D3DRJ9, Q5VW36, Q6ZME1, Q8IZG0, Q96JM8, Q96MS9, Q9BVF3, Q9NX87

    12. XM_017014856.2 → XP_016870345.1  focadhesin isoform X11

    13. XM_047423540.1 → XP_047279496.1  focadhesin isoform X5

    14. XM_024447586.2 → XP_024303354.1  focadhesin isoform X6

      Conserved Domains (2) summary
      pfam11229
      Location:1108 → 1696
      Focadhesin
      pfam12530
      Location:385 → 609
      DUF3730; Protein of unknown function (DUF3730)

    15. XM_017014859.2 → XP_016870348.1  focadhesin isoform X7

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      20669421..21009826
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054363170.1 → XP_054219145.1  focadhesin isoform X4

    2. XM_054363172.1 → XP_054219147.1  focadhesin isoform X2

    3. XM_054363171.1 → XP_054219146.1  focadhesin isoform X4

    4. XM_054363173.1 → XP_054219148.1  focadhesin isoform X5

    5. XM_054363166.1 → XP_054219141.1  focadhesin isoform X1

    6. XM_054363169.1 → XP_054219144.1  focadhesin isoform X3

    7. XM_054363168.1 → XP_054219143.1  focadhesin isoform X2

    8. XM_054363167.1 → XP_054219142.1  focadhesin isoform X14

    9. XM_054363177.1 → XP_054219152.1  focadhesin isoform X15

    10. XM_054363178.1 → XP_054219153.1  focadhesin isoform X16

    11. XM_054363174.1 → XP_054219149.1  focadhesin isoform X6

    12. XM_054363175.1 → XP_054219150.1  focadhesin isoform X6

    13. XM_054363176.1 → XP_054219151.1  focadhesin isoform X7

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5VW36.2 GenPept UniProtKB/Swiss-Prot:Q5VW36

    Gene LinkOut

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

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