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

Gene ID: 57477, updated on 5-Mar-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
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Genomic context

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Location:
Xp11.22
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (50575534..50814194, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (49846979..50085560, complement)
105.20220307 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
  • 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 
Component Evidence Code Pubs
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 intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
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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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_2023_10

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

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