U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from MedGen

    • Showing Current items.

    FAT4 FAT atypical cadherin 4 [ Homo sapiens (human) ]

    Gene ID: 79633, updated on 1-Mar-2024

    Summary

    Official Symbol
    FAT4provided by HGNC
    Official Full Name
    FAT atypical cadherin 4provided by HGNC
    Primary source
    HGNC:HGNC:23109
    See related
    Ensembl:ENSG00000196159 MIM:612411; AllianceGenome:HGNC:23109
    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
    FATJ; FAT-J; CDHF14; CDHR11; HKLLS2; VMLDS2; NBLA00548
    Summary
    The protein encoded by this gene is a member of the protocadherin family. This gene may play a role in regulating planar cell polarity (PCP). Studies in mice suggest that loss of PCP signaling may cause cystic kidney disease, and mutations in this gene have been associated with Van Maldergem Syndrome 2. Alternatively spliced transcript variants have been noted for this gene. [provided by RefSeq, Mar 2014]
    Expression
    Ubiquitous expression in gall bladder (RPKM 2.8), ovary (RPKM 2.6) and 23 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See FAT4 in Genome Data Viewer
    Location:
    4q28.1
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (125314955..125492932)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (128617253..128795252)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (126236110..126414087)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2516 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15668 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr4:125633295-125633860 and GRCh37_chr4:125633861-125634426 Neighboring gene ankyrin repeat domain containing 50 Neighboring gene NANOG hESC enhancer GRCh37_chr4:126189240-126189741 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:126246738-126247342 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:126278491-126279282 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:126279283-126280072 Neighboring gene VISTA enhancer hs1389 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:126482433-126483184 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:126488021-126488685 Neighboring gene microRNA 2054 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:126557979-126558480 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:126558481-126558980 Neighboring gene nucleoporin 58 pseudogene 1

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Hennekam lymphangiectasia-lymphedema syndrome 2
    MedGen: C4014939 OMIM: 616006 GeneReviews: Not available
    Compare labs
    Van Maldergem syndrome 2
    MedGen: C3809875 OMIM: 615546 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

    Description
    A genome-wide study of common SNPs and CNVs in cognitive performance in the CANTAB.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association data of bipolar disorder and major depressive disorder.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ23056, FLJ77878

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in cell-cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in cerebral cortex development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in hippo signaling ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in homophilic cell adhesion via plasma membrane adhesion molecules IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in neurogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    located_in extracellular exosome HDA PubMed 
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    protocadherin Fat 4
    Names
    FAT tumor suppressor homolog 4
    cadherin family member 14
    cadherin-related family member 11
    fat-like cadherin protein FAT-J
    putative protein product of Nbla00548

    NCBI Reference Sequences (RefSeq)

    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_033865.2 RefSeqGene

      Range
      5002..182979
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001291285.3NP_001278214.1  protocadherin Fat 4 isoform 2 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame acceptor splice site at the junction of 3' terminal exon compared to variant 1. The resulting isoform (2) is 1 aa shorter than isoform 1.
      Source sequence(s)
      AC079835, AC092629, AC098865
      UniProtKB/Swiss-Prot
      Q6V0I7
      UniProtKB/TrEMBL
      B3KU84, X2G5I7, X2GA70
      Conserved Domains (4) summary
      cd11304
      Location:21592254
      Cadherin_repeat; Cadherin tandem repeat domain
      cd00054
      Location:38643900
      EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
      cd00110
      Location:39794142
      LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
      pfam00008
      Location:41684198
      EGF; EGF-like domain
    2. NM_001291303.3NP_001278232.1  protocadherin Fat 4 isoform 1 precursor

      See identical proteins and their annotated locations for NP_001278232.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AC079835, AC092629, AC098865
      Consensus CDS
      CCDS93620.1
      UniProtKB/TrEMBL
      A0A6Q8JR05
      Related
      ENSP00000377862.4, ENST00000394329.9
      Conserved Domains (4) summary
      cd11304
      Location:21592254
      Cadherin_repeat; Cadherin tandem repeat domain
      cd00054
      Location:38643900
      EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
      cd00110
      Location:39794142
      LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
      pfam00008
      Location:41684198
      EGF; EGF-like domain
    3. NM_024582.6NP_078858.4  protocadherin Fat 4 isoform 3 precursor

      See identical proteins and their annotated locations for NP_078858.4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate in-frame acceptor splice site at an internal exon compared to variant 1. The resulting isoform (3) is 2 aa shorter than isoform 1.
      Source sequence(s)
      AC079835, AC092629, AC098865
      UniProtKB/Swiss-Prot
      A8K5Z6, B5MDG4, Q3LIA6, Q6V0I7, Q8TCK7, Q9H5T6
      Conserved Domains (4) summary
      cd11304
      Location:21592254
      Cadherin_repeat; Cadherin tandem repeat domain
      cd00054
      Location:38623898
      EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
      cd00110
      Location:39774140
      LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
      pfam00008
      Location:41664196
      EGF; EGF-like domain

    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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      125314955..125492932
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047416151.1XP_047272107.1  protocadherin Fat 4 isoform X2

      UniProtKB/TrEMBL
      A0A6Q8JR05
    2. XM_047416153.1XP_047272109.1  protocadherin Fat 4 isoform X3

    3. XM_011532237.3XP_011530539.1  protocadherin Fat 4 isoform X1

      UniProtKB/TrEMBL
      A0A7P0T1I0
      Related
      ENSP00000501473.2, ENST00000674496.2
      Conserved Domains (4) summary
      cd11304
      Location:416511
      Cadherin_repeat; Cadherin tandem repeat domain
      cd00054
      Location:21212157
      EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
      cd00110
      Location:22362399
      LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
      pfam00008
      Location:24252455
      EGF; EGF-like domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      128617253..128795252
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054350821.1XP_054206796.1  protocadherin Fat 4 isoform X1