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

Summary

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

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_000004.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH120073 (e-PCR)
- UniSTS:133396

SGC34670 (e-PCR)
- UniSTS:45080

D4S789 (e-PCR)
- UniSTS:95267

ShrmL__5406 (e-PCR)
- UniSTS:463920

D4S1166 (e-PCR)
- UniSTS:45127

SHGC-155380 (e-PCR)
- UniSTS:183912

SHGC-155720 (e-PCR)
- UniSTS:183918

D4S2805 (e-PCR)
- UniSTS:10609

SHGC-24718 (e-PCR)
- UniSTS:60031

SHGC-143416 (e-PCR)
- UniSTS:171904

RH120166 (e-PCR)
- UniSTS:132233

G34188 (e-PCR)
- UniSTS:52158

SHGC-51583 (e-PCR)
- UniSTS:27878

D4S2393 (e-PCR), detects polymorphism
- UniSTS:57831

D5S1629E (e-PCR)
- UniSTS:151038

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

NG_028077.1 RefSeqGene

Range

5130..353154

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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