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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
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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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