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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
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Genomic context

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See FOCAD in Genome Data Viewer
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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