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    WASHC4 WASH complex subunit 4 [ Homo sapiens (human) ]

    Gene ID: 23325, updated on 3-Apr-2024

    Summary

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    Official Symbol
    WASHC4provided by HGNC
    Official Full Name
    WASH complex subunit 4provided by HGNC
    Primary source
    HGNC:HGNC:29174
    See related
    Ensembl:ENSG00000136051 MIM:615748; AllianceGenome:HGNC:29174
    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
    SWIP; MRT43; KIAA1033
    Summary
    This gene encodes a component of the WASH complex, which functions in the intracellular transport of endosomes. Mutations in this gene have been detected in individuals with autosomal recessive cognitive disability. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2014]
    Expression
    Ubiquitous expression in lymph node (RPKM 16.8), appendix (RPKM 15.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    12q23.3
    Exon count:
    35
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (105107731..105169130)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (105069550..105130947)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (105501509..105562908)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene aldehyde dehydrogenase 1 family member L2 Neighboring gene uncharacterized LOC124903005 Neighboring gene Sharpr-MPRA regulatory region 9297 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:105477079-105477879 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4803 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:105486286-105486900 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4805 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6940 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4804 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6941 Neighboring gene uncharacterized LOC414300 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:105593258-105593758 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:105593759-105594259 Neighboring gene adaptor protein, phosphotyrosine interacting with PH domain and leucine zipper 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4806 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4807 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:105629835-105630335 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:105639601-105640102 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:105655901-105656075 Neighboring gene C12orf75 antisense RNA 1

    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. Novel KIAA1033/WASHC4 mutations in three patients with syndromic intellectual disability and a review of the literature. Assoum M, et al. Am J Med Genet A, 2020 Apr. PMID 31953988
    2. Identification of a novel candidate gene for non-syndromic autosomal recessive intellectual disability: the WASH complex member SWIP. Ropers F, et al. Hum Mol Genet, 2011 Jul 1. PMID 21498477
    3. Genetic disruption of WASHC4 drives endo-lysosomal dysfunction and cognitive-movement impairments in mice and humans. Courtland JL, et al. Elife, 2021 Mar 22. PMID 33749590, Free PMC Article
    4. The WASH complex, an endosomal Arp2/3 activator, interacts with the Hermansky-Pudlak syndrome complex BLOC-1 and its cargo phosphatidylinositol-4-kinase type IIα. Ryder PV, et al. Mol Biol Cell, 2013 Jul. PMID 23676666, Free PMC Article
    5. Identification of Alzheimer disease-associated variants in genes that regulate retromer function. Vardarajan BN, et al. Neurobiol Aging, 2012 Sep. PMID 22673115, Free PMC Article

    See all (57) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SWIP mediates retromer-independent membrane recruitment of the WASH complex.
      Title: SWIP mediates retromer-independent membrane recruitment of the WASH complex.
    2. Genetic disruption of WASHC4 drives endo-lysosomal dysfunction and cognitive-movement impairments in mice and humans.
      Title: Genetic disruption of WASHC4 drives endo-lysosomal dysfunction and cognitive-movement impairments in mice and humans.
    3. Novel KIAA1033/WASHC4 mutations in three patients with syndromic intellectual disability and a review of the literature.
      Title: Novel KIAA1033/WASHC4 mutations in three patients with syndromic intellectual disability and a review of the literature.
    4. Ten KIAA1033 SNPs were also significantly associated with AD in a group of African Americans.
      Title: Identification of Alzheimer disease-associated variants in genes that regulate retromer function.
    5. SWIP is a novel gene for non-syndromic autosomal recessive intellectual disability
      Title: Identification of a novel candidate gene for non-syndromic autosomal recessive intellectual disability: the WASH complex member SWIP.
    6. WAFL may play an important role in endocytosis and subsequent membrane trafficking by interacting with AP2 through KIAA0196 and KIAA1033
      Title: The ulcerative colitis marker protein WAFL interacts with accessory proteins in endocytosis.
    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
    Intellectual disability, autosomal recessive 43
    MedGen: C4014386 OMIM: 615817 GeneReviews: Not available
    		Compare labs

    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    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 endosomal transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within endosomal transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in endosomal transport ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in endosomal transport NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in endosome organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in endosome organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in nuclear envelope budding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of Arp2/3 complex-mediated actin nucleation NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of BLOC-1 complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of WASH complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of WASH complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of WASH complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in early endosome membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    is_active_in endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    WASH complex subunit 4
    Names
    WASH complex subunit 7
    WASH complex subunit SWIP
    strumpellin and WASH-interacting protein

    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.

    Genomic

    1. NG_034157.1 RefSeqGene

      Range
      5018..66417
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001293640.2 → NP_001280569.1  WASH complex subunit 4 isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AK001657, AL137753, BC040936, BC143373
      Consensus CDS
      CCDS73514.1
      UniProtKB/TrEMBL
      A0A087X256, B7ZKT9
      Related
      ENSP00000484713.1, ENST00000620430.5
      Conserved Domains (3) summary
      pfam14744
      Location:613 → 946
      WASH-7_mid; WASH complex subunit 7
      pfam14745
      Location:32 → 601
      WASH-7_N; WASH complex subunit 7, N-terminal
      pfam14746
      Location:967 → 1136
      WASH-7_C; WASH complex subunit 7, C-terminal

    2. NM_015275.3 → NP_056090.1  WASH complex subunit 4 isoform 2

      See identical proteins and their annotated locations for NP_056090.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AB028956, AK001657, AL137753, BC040936
      Consensus CDS
      CCDS41826.1
      UniProtKB/Swiss-Prot
      Q2M389, Q2NL83, Q8IW61, Q8N5W7, Q9NVD6, Q9UPW7
      UniProtKB/TrEMBL
      B7ZKT9
      Related
      ENSP00000328062.6, ENST00000332180.10
      Conserved Domains (3) summary
      pfam14744
      Location:612 → 945
      WASH-7_mid; WASH complex subunit 7
      pfam14745
      Location:32 → 600
      WASH-7_N; WASH complex subunit 7, N-terminal
      pfam14746
      Location:966 → 1135
      WASH-7_C; WASH complex subunit 7, C-terminal

    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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      105107731..105169130
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011538073.4 → XP_011536375.1  WASH complex subunit 4 isoform X1

      UniProtKB/TrEMBL
      B7ZKT9
      Conserved Domains (3) summary
      pfam14744
      Location:612 → 900
      WASH-7_mid; WASH complex subunit 7
      pfam14745
      Location:32 → 600
      WASH-7_N; WASH complex subunit 7, N-terminal
      pfam14746
      Location:921 → 1090
      WASH-7_C; WASH complex subunit 7, C-terminal

    2. XM_047428593.1 → XP_047284549.1  WASH complex subunit 4 isoform X5

      Related
      ENST00000311317.8

    3. XM_017019082.3 → XP_016874571.1  WASH complex subunit 4 isoform X4

      Conserved Domains (2) summary
      pfam14744
      Location:612 → 920
      WASH-7_mid; WASH complex subunit 7
      pfam14745
      Location:32 → 600
      WASH-7_N; WASH complex subunit 7, N-terminal

    4. XM_047428592.1 → XP_047284548.1  WASH complex subunit 4 isoform X3

    5. XM_011538074.3 → XP_011536376.1  WASH complex subunit 4 isoform X2

      See identical proteins and their annotated locations for XP_011536376.1

      UniProtKB/TrEMBL
      B7ZKT9
      Conserved Domains (3) summary
      pfam14744
      Location:424 → 757
      WASH-7_mid; WASH complex subunit 7
      pfam14745
      Location:1 → 412
      WASH-7_N; WASH complex subunit 7, N-terminal
      pfam14746
      Location:778 → 947
      WASH-7_C; WASH complex subunit 7, C-terminal

    RNA

    1. XR_007063060.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      105069550..105130947
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054371555.1 → XP_054227530.1  WASH complex subunit 4 isoform X1

    2. XM_054371559.1 → XP_054227534.1  WASH complex subunit 4 isoform X5

    3. XM_054371558.1 → XP_054227533.1  WASH complex subunit 4 isoform X4

    4. XM_054371557.1 → XP_054227532.1  WASH complex subunit 4 isoform X3

    5. XM_054371556.1 → XP_054227531.1  WASH complex subunit 4 isoform X2

    RNA

    1. XR_008488552.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q2M389.2 GenPept UniProtKB/Swiss-Prot:Q2M389

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