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    WASHC2A WASH complex subunit 2A [ Homo sapiens (human) ]

    Gene ID: 387680, updated on 3-Apr-2024

    Summary

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    Official Symbol
    WASHC2Aprovided by HGNC
    Official Full Name
    WASH complex subunit 2Aprovided by HGNC
    Primary source
    HGNC:HGNC:23416
    See related
    Ensembl:ENSG00000099290 AllianceGenome:HGNC:23416
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    FAM21A; FAM21B; bA98I6.1; bA56A21.1
    Summary
    Predicted to enable phosphatidylinositol phosphate binding activity and retromer complex binding activity. Involved in protein localization to endosome. Located in cytosol and nucleolus. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in heart (RPKM 26.3), bone marrow (RPKM 21.0) and 25 other tissues See more
    Orthologs
    all
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    Genomic context

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    Location:
    10q11.23
    Exon count:
    33
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (50067954..50133509)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (50917598..50983160)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (51827714..51893269)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene TIMM23B-AGAP6 readthrough (NMD candidate) Neighboring gene ArfGAP with GTPase domain, ankyrin repeat and PH domain 6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:51784655-51785155 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:51787127-51787626 Neighboring gene family with sequence similarity 21, member A pseudogene Neighboring gene solute carrier family 9 member 3 pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2365 Neighboring gene solute carrier family 9 member 3 pseudogene 1 Neighboring gene N-acylsphingosine amidohydrolase 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2366 Neighboring gene Sharpr-MPRA regulatory region 2427

    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. FAM21 directs SNX27-retromer cargoes to the plasma membrane by preventing transport to the Golgi apparatus. Lee S, et al. Nat Commun, 2016 Mar 9. PMID 26956659, Free PMC Article
    2. Nuclear IGF1R Interacts with Regulatory Regions of Chromatin to Promote RNA Polymerase II Recruitment and Gene Expression Associated with Advanced Tumor Stage. Aleksic T, et al. Cancer Res, 2018 Jul 1. PMID 29735545, Free PMC Article
    3. Identification of a novel Rev-interacting cellular protein. Kramer-Hämmerle S, et al. BMC Cell Biol, 2005 Apr 24. PMID 15847701, Free PMC Article
    4. Control of HIV replication in astrocytes by a family of highly conserved host proteins with a common Rev-interacting domain (Risp). Vincendeau M, et al. AIDS, 2010 Oct 23. PMID 20827171
    5. TBC1D23 is a bridging factor for endosomal vesicle capture by golgins at the trans-Golgi. Shin JJH, et al. Nat Cell Biol, 2017 Dec. PMID 29084197, Free PMC Article

    See all (56) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. FAM21 interacts with Ku to promote the localization of WASH to DNA double strand break sites.
      Title: FAM21 interacts with Ku to promote the localization of WASH to DNA double strand break sites.
    2. Study reports that nuclear IGF1R associates with advanced tumor stage and is recruited selectively to regulatory regions of chromatin including JUN and FAM21A promoters. JUN and FAM21A identified as mediators of cell survival and IGF-induced migration, properties that tumors require to attain advanced stage.
      Title: Nuclear IGF1R Interacts with Regulatory Regions of Chromatin to Promote RNA Polymerase II Recruitment and Gene Expression Associated with Advanced Tumor Stage.
    3. SNX27 interaction with FAM21 is required for the precise localization of SNX27 at an endosomal subdomain.
      Title: FAM21 directs SNX27-retromer cargoes to the plasma membrane by preventing transport to the Golgi apparatus.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    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

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Pr55(Gag) gag Expression of the Risp family decreases the amounts of HIV-1 Gag expression in infected astrocytes PubMed
    Rev rev Expression of the Risp family in human brain tissues and astrocytes can inhibit Rev activity by inducing accumulation of Rev in the cytoplasm PubMed
    rev Co-localization of human 16.4.1 and HIV-1 Rev is demonstrated by epifluorescence microscopy of HeLa 16.4.1-GFP cells transfected with a Rev-CFP expression construct PubMed
    rev Yeast-two hybrid screening and mammalian two-hybrid assays show the interaction of human 16.4.1 protein with HIV-1 Rev; amino acid residues 38-39 and 59-60 in Rev interact with a 95 amino acid region (residues 39-133) in a human protein fragment 16.4.1 PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ18670, FLJ43157, KIAA0592

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables phosphatidylinositol phosphate binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables retromer complex binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in endosomal transport NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in protein localization to endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein localization to endosome IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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 
    involved_in retrograde transport, endosome to Golgi IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in retrograde transport, endosome to Golgi ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    part_of WASH complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of WASH complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    part_of WASH complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in early endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in early endosome ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in early endosome membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    WASH complex subunit 2A
    Names
    WASH complex subunit FAM21A
    WASH complex subunit FAM21B
    alternative protein FAM21B
    family with sequence similarity 21 member A
    family with sequence similarity 21, member B

    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_001005751.3 → NP_001005751.1  WASH complex subunit 2A isoform 1

      See identical proteins and their annotated locations for NP_001005751.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      BC065500, BC075815, BC082258, DC336167
      Consensus CDS
      CCDS41527.1
      UniProtKB/Swiss-Prot
      A2A3S2, A2A3U6, Q5SNT6, Q641Q2, Q6DHY0
      UniProtKB/TrEMBL
      B7ZME8
      Related
      ENSP00000282633.5, ENST00000282633.10
      Conserved Domains (1) summary
      pfam15255
      Location:949 → 1076
      CAP-ZIP_m; WASH complex subunit CAP-Z interacting, central region

    2. NM_001291398.2 → NP_001278327.1  WASH complex subunit 2A isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the central coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.
      Source sequence(s)
      BC065500, BC075815, BC082258, DC336167
      Consensus CDS
      CCDS76303.1
      UniProtKB/TrEMBL
      B7ZME8
      Related
      ENSP00000344037.6, ENST00000351071.11
      Conserved Domains (1) summary
      pfam15255
      Location:930 → 1055
      CAP-ZIP_m; WASH complex subunit CAP-Z interacting, central region

    3. NM_001330102.2 → NP_001317031.1  WASH complex subunit 2A isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks two alternate in-frame exons in the 3' coding region compared to variant 1. It encodes isoform 3, which is shorter than isoform 1.
      Source sequence(s)
      AL442003, AL450382, BC065500
      Consensus CDS
      CCDS81463.1
      UniProtKB/TrEMBL
      B7ZME8, E7ESD2
      Related
      ENSP00000314417.7, ENST00000314664.12
      Conserved Domains (1) summary
      pfam15255
      Location:889 → 1014
      CAP-ZIP_m; WASH complex subunit CAP-Z interacting, central region

    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_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      50067954..50133509
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017016227.2 → XP_016871716.1  WASH complex subunit 2A isoform X3

      UniProtKB/TrEMBL
      B7ZME8

    2. XM_011539786.3 → XP_011538088.1  WASH complex subunit 2A isoform X20

      UniProtKB/TrEMBL
      B7ZME8
      Conserved Domains (1) summary
      pfam15255
      Location:886 → 943
      CAP-ZIP_m; WASH complex subunit CAP-Z interacting, central region

    3. XM_006717831.4 → XP_006717894.2  WASH complex subunit 2A isoform X6

      UniProtKB/TrEMBL
      B7ZME8
      Conserved Domains (1) summary
      pfam15255
      Location:898 → 1025
      CAP-ZIP_m; WASH complex subunit CAP-Z interacting, central region

    4. XM_017016231.2 → XP_016871720.1  WASH complex subunit 2A isoform X9

      UniProtKB/TrEMBL
      B7ZME8

    5. XM_047425212.1 → XP_047281168.1  WASH complex subunit 2A isoform X15

    6. XM_047425214.1 → XP_047281170.1  WASH complex subunit 2A isoform X18

    7. XM_047425217.1 → XP_047281173.1  WASH complex subunit 2A isoform X22

    8. XM_005269807.4 → XP_005269864.2  WASH complex subunit 2A isoform X2

      UniProtKB/TrEMBL
      B7ZME8
      Conserved Domains (1) summary
      pfam15255
      Location:920 → 1047
      CAP-ZIP_m; WASH complex subunit CAP-Z interacting, central region

    9. XM_017016229.2 → XP_016871718.1  WASH complex subunit 2A isoform X5

      UniProtKB/TrEMBL
      B7ZME8

    10. XM_047425207.1 → XP_047281163.1  WASH complex subunit 2A isoform X8

    11. XM_047425211.1 → XP_047281167.1  WASH complex subunit 2A isoform X14

    12. XM_047425216.1 → XP_047281172.1  WASH complex subunit 2A isoform X21

    13. XM_047425209.1 → XP_047281165.1  WASH complex subunit 2A isoform X12

    14. XM_047425213.1 → XP_047281169.1  WASH complex subunit 2A isoform X17

    15. XM_005269806.4 → XP_005269863.2  WASH complex subunit 2A isoform X1

      UniProtKB/TrEMBL
      B7ZME8
      Conserved Domains (1) summary
      pfam15255
      Location:925 → 1052
      CAP-ZIP_m; WASH complex subunit CAP-Z interacting, central region

    16. XM_017016228.2 → XP_016871717.1  WASH complex subunit 2A isoform X4

      UniProtKB/TrEMBL
      B7ZME8

    17. XM_047425210.1 → XP_047281166.1  WASH complex subunit 2A isoform X13

    18. XM_047425208.1 → XP_047281164.1  WASH complex subunit 2A isoform X11

    19. XM_006717832.4 → XP_006717895.2  WASH complex subunit 2A isoform X16

      UniProtKB/TrEMBL
      A0A087WYF6, B7ZME8
      Related
      ENSP00000481763.1, ENST00000611324.4
      Conserved Domains (1) summary
      pfam15255
      Location:855 → 980
      CAP-ZIP_m; WASH complex subunit CAP-Z interacting, central region

    20. XM_047425206.1 → XP_047281162.1  WASH complex subunit 2A isoform X7

    21. XM_017016232.2 → XP_016871721.1  WASH complex subunit 2A isoform X10

      UniProtKB/TrEMBL
      B7ZME8

    22. XM_047425215.1 → XP_047281171.1  WASH complex subunit 2A isoform X19

    23. XM_047425219.1 → XP_047281175.1  WASH complex subunit 2A isoform X25

    24. XM_047425220.1 → XP_047281176.1  WASH complex subunit 2A isoform X28

    25. XM_047425218.1 → XP_047281174.1  WASH complex subunit 2A isoform X24

    26. XM_017016233.2 → XP_016871722.1  WASH complex subunit 2A isoform X23

      UniProtKB/TrEMBL
      F8W7U3
      Related
      ENSP00000382277.2, ENST00000399339.6

    27. XM_024447991.2 → XP_024303759.1  WASH complex subunit 2A isoform X26

      Conserved Domains (1) summary
      pfam15255
      Location:314 → 450
      CAP-ZIP_m; WASH complex subunit CAP-Z interacting, central region

    28. XM_005269810.4 → XP_005269867.2  WASH complex subunit 2A isoform X27

      Conserved Domains (1) summary
      pfam15255
      Location:317 → 444
      CAP-ZIP_m; WASH complex subunit CAP-Z interacting, central region

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      50917598..50983160
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054365854.1 → XP_054221829.1  WASH complex subunit 2A isoform X3

    2. XM_054365871.1 → XP_054221846.1  WASH complex subunit 2A isoform X20

    3. XM_054365857.1 → XP_054221832.1  WASH complex subunit 2A isoform X6

    4. XM_054365860.1 → XP_054221835.1  WASH complex subunit 2A isoform X9

    5. XM_054365866.1 → XP_054221841.1  WASH complex subunit 2A isoform X15

    6. XM_054365869.1 → XP_054221844.1  WASH complex subunit 2A isoform X18

    7. XM_054365873.1 → XP_054221848.1  WASH complex subunit 2A isoform X22

    8. XM_054365853.1 → XP_054221828.1  WASH complex subunit 2A isoform X2

    9. XM_054365856.1 → XP_054221831.1  WASH complex subunit 2A isoform X5

    10. XM_054365859.1 → XP_054221834.1  WASH complex subunit 2A isoform X8

    11. XM_054365865.1 → XP_054221840.1  WASH complex subunit 2A isoform X14

    12. XM_054365872.1 → XP_054221847.1  WASH complex subunit 2A isoform X21

    13. XM_054365863.1 → XP_054221838.1  WASH complex subunit 2A isoform X12

    14. XM_054365868.1 → XP_054221843.1  WASH complex subunit 2A isoform X17

    15. XM_054365852.1 → XP_054221827.1  WASH complex subunit 2A isoform X1

    16. XM_054365855.1 → XP_054221830.1  WASH complex subunit 2A isoform X4

    17. XM_054365864.1 → XP_054221839.1  WASH complex subunit 2A isoform X13

    18. XM_054365862.1 → XP_054221837.1  WASH complex subunit 2A isoform X11

    19. XM_054365867.1 → XP_054221842.1  WASH complex subunit 2A isoform X16

    20. XM_054365858.1 → XP_054221833.1  WASH complex subunit 2A isoform X7

    21. XM_054365861.1 → XP_054221836.1  WASH complex subunit 2A isoform X10

    22. XM_054365870.1 → XP_054221845.1  WASH complex subunit 2A isoform X19

    23. XM_054365876.1 → XP_054221851.1  WASH complex subunit 2A isoform X25

    24. XM_054365879.1 → XP_054221854.1  WASH complex subunit 2A isoform X28

    25. XM_054365875.1 → XP_054221850.1  WASH complex subunit 2A isoform X24

    26. XM_054365874.1 → XP_054221849.1  WASH complex subunit 2A isoform X23

    27. XM_054365877.1 → XP_054221852.1  WASH complex subunit 2A isoform X26

    28. XM_054365878.1 → XP_054221853.1  WASH complex subunit 2A isoform X27

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_018232.1: Suppressed sequence

      Description
      NM_018232.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q641Q2.3 GenPept UniProtKB/Swiss-Prot:Q641Q2

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