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    SHROOM4 shroom family member 4 [ Homo sapiens (human) ]

    Gene ID: 57477, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SHROOM4provided by HGNC
    Official Full Name
    shroom family member 4provided by HGNC
    Primary source
    HGNC:HGNC:29215
    See related
    Ensembl:ENSG00000158352 MIM:300579; AllianceGenome:HGNC:29215
    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
    SHAP; shrm4; MRXSSDS
    Summary
    This gene encodes a member of the APX/Shroom family, which contain an N-terminal PDZ domain and a C-terminal ASD2 motif. The encoded protein may play a role in cytoskeletal architecture. Mutations in this gene have been linked to the X-linked Stocco dos Santos syndrome characterized by cognitive disabilities. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jul 2017]
    Expression
    Broad expression in lung (RPKM 5.3), fat (RPKM 2.8) and 19 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SHROOM4 in Genome Data Viewer
    Location:
    Xp11.22
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (50575534..50814194, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (49846979..50085560, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (50329796..50557194, complement)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene cyclin B3 Neighboring gene diacylglycerol kinase kappa Neighboring gene Sharpr-MPRA regulatory region 2913 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:50212987-50213784 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:50324379-50325149 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:50377907-50378408 Neighboring gene RNA, U6 small nuclear 935, pseudogene Neighboring gene NANOG hESC enhancer GRCh37_chrX:50440638-50441169 Neighboring gene NANOG hESC enhancer GRCh37_chrX:50469171-50469706 Neighboring gene Sharpr-MPRA regulatory region 11230 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:50556241-50556742 Neighboring gene H3 histone pseudogene 44 Neighboring gene bone morphogenetic protein 15

    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 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. Stocco dos Santos X-linked mental retardation syndrome: clinical elucidation and localization to Xp11.3-Xq21.3. Stocco dos Santos RC, et al. Am J Med Genet A, 2003 Apr 30. PMID 12673656
    2. Epilepsy and intellectual disability linked protein Shrm4 interaction with GABA(B)Rs shapes inhibitory neurotransmission. Zapata J, et al. Nat Commun, 2017 Mar 6. PMID 28262662, Free PMC Article
    3. X-linked variations in SHROOM4 are implicated in congenital anomalies of the urinary tract and the anorectal, cardiovascular and central nervous systems. Kolvenbach CM, et al. J Med Genet, 2023 Jun. PMID 36379543, Free PMC Article
    4. Disruptions of the novel KIAA1202 gene are associated with X-linked mental retardation. Hagens O, et al. Hum Genet, 2006 Jan. PMID 16249884
    5. A new standard nomenclature for proteins related to Apx and Shroom. Hagens O, et al. BMC Cell Biol, 2006 Apr 14. PMID 16615870, Free PMC Article

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. X-linked variations in SHROOM4 are implicated in congenital anomalies of the urinary tract and the anorectal, cardiovascular and central nervous systems.
      Title: X-linked variations in SHROOM4 are implicated in congenital anomalies of the urinary tract and the anorectal, cardiovascular and central nervous systems.
    2. Shrm4 interaction with GABA-B receptors shapes inhibitory neurotransmission.
      Title: Epilepsy and intellectual disability linked protein Shrm4 interaction with GABA(B)Rs shapes inhibitory neurotransmission.
    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

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    No evidence available (Last evaluated 2012-10-10)

    ClinGen Genome Curation Page
    Triplosensitivity

    No evidence available (Last evaluated 2012-10-10)

    ClinGen Genome Curation Page

    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

    Clone Names

    • KIAA1202

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables actin filament binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables actin filament binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables myosin II binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in actin cytoskeleton organization NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in actin filament organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in actin filament organization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in brain development IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    NOT involved_in cell morphogenesis IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in cognition IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of postsynaptic membrane neurotransmitter receptor levels IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in GABA-ergic synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    colocalizes_with actin cytoskeleton ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in actin filament IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in adherens junction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in apical junction complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in apical plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in apical plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in basal plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in cortical actin cytoskeleton IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    colocalizes_with cortical actin cytoskeleton ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytoplasmic side of plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in focal adhesion IDA
    Inferred from Direct Assay
    more info
    		  
    located_in glutamatergic synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in postsynapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in presynapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    colocalizes_with stress fiber ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    protein Shroom4
    Names
    second homolog of apical protein

    NCBI Reference Sequences (RefSeq)

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    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_011882.2 RefSeqGene

      Range
      5000..232398
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_020717.5 → NP_065768.2  protein Shroom4

      See identical proteins and their annotated locations for NP_065768.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the functional protein.
      Source sequence(s)
      AC233286, AL121865, AL359272
      Consensus CDS
      CCDS35277.1
      UniProtKB/Swiss-Prot
      A7E2X9, D6RFW0, Q96LA0, Q9ULL8
      Related
      ENSP00000365188.2, ENST00000376020.9
      Conserved Domains (2) summary
      cd00992
      Location:13 → 89
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      pfam08687
      Location:1247 → 1485
      ASD2; Apx/Shroom domain ASD2

    RNA

    1. NR_027121.3 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site at its 3' end compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC233286, AL121865, AL359272

    2. NR_172068.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC233286, AL121865, AL359272

    3. NR_172069.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC233286, AL121865

    4. NR_172070.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC233286, AL121865

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      50575534..50814194 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047442279.1 → XP_047298235.1  protein Shroom4 isoform X3

    2. XM_017029683.2 → XP_016885172.1  protein Shroom4 isoform X2

    3. XM_017029682.3 → XP_016885171.1  protein Shroom4 isoform X1

    4. XM_017029684.2 → XP_016885173.1  protein Shroom4 isoform X4

      Related
      ENSP00000421450.1, ENST00000460112.3

    5. XM_017029685.3 → XP_016885174.1  protein Shroom4 isoform X5

    6. XM_047442280.1 → XP_047298236.1  protein Shroom4 isoform X7

    7. XM_017029687.3 → XP_016885176.1  protein Shroom4 isoform X6

    RNA

    1. XR_007068197.1 RNA Sequence

    2. XR_007068196.1 RNA Sequence

    3. XR_001755718.3 RNA Sequence

    4. XR_001755717.3 RNA Sequence

    5. XR_001755716.3 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      49846979..50085560 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054327437.1 → XP_054183412.1  protein Shroom4 isoform X3

    2. XM_054327436.1 → XP_054183411.1  protein Shroom4 isoform X2

    3. XM_054327435.1 → XP_054183410.1  protein Shroom4 isoform X1

    4. XM_054327438.1 → XP_054183413.1  protein Shroom4 isoform X4

    5. XM_054327439.1 → XP_054183414.1  protein Shroom4 isoform X5

    6. XM_054327441.1 → XP_054183416.1  protein Shroom4 isoform X7

    7. XM_054327440.1 → XP_054183415.1  protein Shroom4 isoform X6

    RNA

    1. XR_008485502.1 RNA Sequence

    2. XR_008485501.1 RNA Sequence

    3. XR_008485500.1 RNA Sequence

    4. XR_008485499.1 RNA Sequence

    5. XR_008485498.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9ULL8.3 GenPept UniProtKB/Swiss-Prot:Q9ULL8

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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