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    SHROOM3 shroom family member 3 [ Homo sapiens (human) ]

    Gene ID: 57619, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SHROOM3provided by HGNC
    Official Full Name
    shroom family member 3provided by HGNC
    Primary source
    HGNC:HGNC:30422
    See related
    Ensembl:ENSG00000138771 MIM:604570; AllianceGenome:HGNC:30422
    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
    SHRM; APXL3; ShrmL; MSTP013
    Summary
    This gene encodes a PDZ-domain-containing protein that belongs to a family of Shroom-related proteins. This protein may be involved in regulating cell shape in certain tissues. A similar protein in mice is required for proper neurulation. [provided by RefSeq, Jan 2011]
    Expression
    Broad expression in colon (RPKM 6.8), gall bladder (RPKM 5.4) and 20 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SHROOM3 in Genome Data Viewer
    Location:
    4q21.1
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (76435229..76783253)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (79775956..80123954)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (77356382..77704406)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene coiled-coil domain containing 158 Neighboring gene small nucleolar RNA SNORD50 Neighboring gene ribosomal protein L36a pseudogene 18 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr4:77379997-77381196 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:77398744-77399474 Neighboring gene RNA, U6 small nuclear 145, pseudogene Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:77479863-77480494 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21629 Neighboring gene microRNA 548ah Neighboring gene microRNA 4450 Neighboring gene uncharacterized LOC105377290 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:77585909-77587108 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr4:77610214-77610736 Neighboring gene SUMO2 pseudogene 11 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:77618582-77619300 Neighboring gene SHROOM3 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 6551 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15489 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:77702656-77703855 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15490 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15491 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15492 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:77707749-77708250 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:77708251-77708750 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:77722401-77723191 Neighboring gene uncharacterized LOC124900719 Neighboring gene putative uncharacterized protein encoded by LINC00596

    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. Mouse models for neural tube closure defects. Juriloff DM, et al. Hum Mol Genet, 2000 Apr 12. PMID 10767323
    2. Loss-of-function de novo mutations play an important role in severe human neural tube defects. Lemay P, et al. J Med Genet, 2015 Jul. PMID 25805808
    3. A homozygous pathogenic variant in SHROOM3 associated with anencephaly and cleft lip and palate. Deshwar AR, et al. Clin Genet, 2020 Sep. PMID 32621286
    4. SHROOM3 is a novel candidate for heterotaxy identified by whole exome sequencing. Tariq M, et al. Genome Biol, 2011 Sep 21. PMID 21936905, Free PMC Article
    5. Identification of interacting genes in genome-wide association studies using a model-based two-stage approach. Zhang Z, et al. Ann Hum Genet, 2010 Sep 1. PMID 20636464, Free PMC Article

    See all (79) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A homozygous pathogenic variant in SHROOM3 associated with anencephaly and cleft lip and palate.
      Title: A homozygous pathogenic variant in SHROOM3 associated with anencephaly and cleft lip and palate.
    2. The three genes associated with chronic kidney disease (AGT, GLO1, and SHROOM3) showed associations with both the high levels of oxidatively damaged DNA and genomic instability.
      Title: Loci associated with genomic damage levels in chronic kidney disease patients and controls.
    3. We confirmed the interaction of endogenous SHROOM3 with FYN in podocytes via a critical Src homology 3-binding domain, distinct from its ROCK-binding domain. Shroom3-Fyn interaction was required in vitro and in vivo for activation of Fyn kinase and downstream nephrin phosphorylation in podocytes.
      Title: SHROOM3-FYN Interaction Regulates Nephrin Phosphorylation and Affects Albuminuria in Allografts.
    4. We determined that coding variant P1244L attenuates the interaction of SHROOM3 with 14-3-3, suggesting alterations to the Hippo pathway, a known mediator of CKD.
      Title: Characterization of Coding/Noncoding Variants for SHROOM3 in Patients with CKD.
    5. Functional variants were further confirmed by western blot and the mammalian two-hybrid assays. Loss of function (LoF) variants were identified in SHROOM3. We observed 1.56 times as many rare [minor allele frequency (MAF) < 0.01] coding variants (p = 2.9 x 10(-3)) in SHROOM genes, and 4.5 times as many rare D-Mis (deleterious missense) variants in SHROOM2 genes in the Neural tube defects cases compared with the controls
      Title: Genetic and functional analysis of SHROOM1-4 in a Chinese neural tube defect cohort.
    6. Two protein-truncating de novo mutations in two independent cases in SHROOM3 strongly implicates this protein in severe human neural tube defects.
      Title: Loss-of-function de novo mutations play an important role in severe human neural tube defects.
    7. variants disrupting the actin-binding domain of SHROOM3 may cause podocyte effacement and impairment of the glomerular filtration barrier
      Title: Shroom3 contributes to the maintenance of the glomerular filtration barrier integrity.
    8. The SNP rs17319721 functions as a cis-acting expression quantitative trait locus of SHROOM3 that facilitates TGF-B1 signaling and contributes to allograft injury.
      Title: Intronic locus determines SHROOM3 expression and potentiates renal allograft fibrosis.
    9. RESULTS: rs1260326 in GCKR (beta=1.30, P = 3.23E-03), rs17319721 in SHROOM3 (beta = -1.28, P-value = 3.18E-03) and rs12917707 in UMOD (beta = 2.0, P-value = 8.84E-04) were significantly associated with baseline estimated GFR
      Title: Investigation of known estimated glomerular filtration rate loci in patients with type 2 diabetes.
    10. A recessive missense mutation in SHROOM3 is associated with heterotaxy syndrome.
      Title: SHROOM3 is a novel candidate for heterotaxy identified by whole exome sequencing.
    Submit: New GeneRIF Correction See all GeneRIFs (14)

    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

    EBI GWAS Catalog

    Description
    Common variants at 5q22 associate with pediatric eosinophilic esophagitis.
    EBI GWAS Catalog
    Genetic loci influencing kidney function and chronic kidney disease.
    EBI GWAS Catalog
    Genome-wide association studies of serum magnesium, potassium, and sodium concentrations identify six Loci influencing serum magnesium levels.
    EBI GWAS Catalog
    Meta-analysis identifies multiple loci associated with kidney function-related traits in east Asian populations.
    EBI GWAS Catalog
    Multiple loci associated with indices of renal function and chronic kidney disease.
    EBI GWAS Catalog
    New loci associated with kidney function and chronic kidney disease.
    EBI GWAS Catalog
    Using multiple measures for quantitative trait association analyses: application to estimated glomerular filtration rate.
    EBI GWAS Catalog

    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

    • KIAA1481, AC107072.2

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables actin filament binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in actin filament organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in apical protein localization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in cell morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in cellular pigment accumulation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in pattern specification process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of cell shape IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in adherens junction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in adherens junction ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in apical junction complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in apical junction complex ISS
    Inferred from Sequence or Structural Similarity
    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
    		  
    is_active_in cortical actin cytoskeleton IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoskeleton ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in microtubule IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    protein Shroom3
    Names
    F-actin-binding protein
    shroom-related 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_028077.1 RefSeqGene

      Range
      5130..353154
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_020859.4 → NP_065910.3  protein Shroom3

      See identical proteins and their annotated locations for NP_065910.3

      Status: REVIEWED

      Source sequence(s)
      AB055660, AC107072, AK127929, AK128677, AW025141
      Consensus CDS
      CCDS3579.2
      UniProtKB/Swiss-Prot
      Q5QTQ3, Q6ZRW3, Q8TF72, Q96IR9, Q9P247
      UniProtKB/TrEMBL
      A0A2R8Y5P9
      Related
      ENSP00000296043.6, ENST00000296043.7
      Conserved Domains (3) summary
      cd00992
      Location:33 → 107
      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:1671 → 1955
      ASD2; Apx/Shroom domain ASD2
      pfam08688
      Location:884 → 1062
      ASD1; Apx/Shroom domain ASD1

    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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      76435229..76783253
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      79775956..80123954
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8TF72.2 GenPept UniProtKB/Swiss-Prot:Q8TF72

    Gene LinkOut

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

    Chemical Information
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