SHROOM3

shroom family member 3, the group of MicroRNA protein coding host genes|Shroom family|PDZ domain containing

Basic information

Region (hg38): 4:76435228-76783253

Links

ENSG00000138771 ∙ NCBI:57619 ∙ OMIM:604570 ∙ HGNC:30422 ∙ Uniprot:Q8TF72 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SHROOM3 gene.

• Inborn genetic diseases (82 variants)
• not provided (46 variants)
• not specified (9 variants)
• SHROOM3-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SHROOM3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				4	8	12
missense			79	15	12	106
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					15	15
Total	0	0	79	19	35

Variants in SHROOM3

This is a list of pathogenic ClinVar variants found in the SHROOM3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
4-76436045-T-A		SHROOM3-related disorder	Benign (Sep 25, 2019)
4-76436063-C-A		not specified	Uncertain significance (Jan 17, 2024)
4-76436120-G-A		not specified	Uncertain significance (Dec 21, 2022)
4-76436126-A-G		not specified	Uncertain significance (Dec 07, 2021)
4-76436140-G-A		not specified	Uncertain significance (May 17, 2023)
4-76436338-C-CT			Benign (Nov 12, 2018)
4-76436339-C-A			Benign (Nov 12, 2018)
4-76436345-G-T			Benign (Nov 12, 2018)
4-76436344-T-TAAA			Benign (Nov 12, 2018)
4-76436375-G-T			Benign (Nov 12, 2018)
4-76436439-T-C			Benign (Jun 19, 2021)
4-76447694-G-A			Benign (Jul 13, 2018)
4-76555619-G-T		not specified • SHROOM3-related disorder	Benign/Likely benign (May 04, 2022)
4-76555636-C-G		not specified	Likely benign (Dec 19, 2022)
4-76555656-T-C		SHROOM3-related disorder	Benign (Dec 31, 2019)
4-76555756-G-C		SHROOM3-related disorder	Likely benign (Aug 29, 2022)
4-76555759-C-T		not specified	Uncertain significance (Aug 09, 2021)
4-76710233-C-A		not specified	Uncertain significance (Feb 26, 2024)
4-76710238-C-T		not specified	Uncertain significance (Oct 26, 2022)
4-76710250-G-A		not specified	Uncertain significance (Dec 27, 2022)
4-76710272-T-A		SHROOM3-related disorder	Benign (Mar 18, 2019)
4-76710274-C-T			Uncertain significance (Mar 01, 2023)
4-76730904-G-C		SHROOM3-related disorder	Benign (May 22, 2019)
4-76731066-T-C			Benign (Jun 19, 2021)
4-76738783-A-C		not specified	Uncertain significance (Dec 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SHROOM3	protein_coding	protein_coding	ENST00000296043	11	348154

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.317	0.683	123704	0	2044	125748	0.00816

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.24	1037	1.16e+3	0.897	0.0000721	12833
Missense in Polyphen		269	323.63	0.83119		3763
Synonymous	1.39	455	494	0.920	0.0000330	4224
Loss of Function	5.79	15	65.6	0.229	0.00000387	739

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0337	0.0333
Ashkenazi Jewish	0.00359	0.00358
East Asian	0.0106	0.0105
Finnish	0.0109	0.0109
European (Non-Finnish)	0.00834	0.00828
Middle Eastern	0.0106	0.0105
South Asian	0.000458	0.000457
Other	0.0101	0.00998

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Controls cell shape changes in the neuroepithelium during neural tube closure. Induces apical constriction in epithelial cells by promoting the apical accumulation of F-actin and myosin II, and probably by bundling stress fibers. Induces apicobasal cell elongation by redistributing gamma-tubulin and directing the assembly of robust apicobasal microtubule arrays (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.100

Intolerance Scores

• loftool: 0.425
• rvis_EVS: 1.4
• rvis_percentile_EVS: 94.73

Haploinsufficiency Scores

• pHI: 0.252
• hipred: N
• hipred_score: 0.403
• ghis: 0.489

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.381

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Shroom3
• Phenotype: digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); skeleton phenotype; embryo phenotype; liver/biliary system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); craniofacial phenotype; growth/size/body region phenotype

Zebrafish Information Network

• Gene name: shroom3
• Affected structure: pronephric glomerular basement membrane
• Phenotype tag: abnormal
• Phenotype quality: increased permeability

Gene ontology

• Biological process: cell morphogenesis;neural tube closure;epithelial cell development;actin filament organization;pattern specification process;regulation of cell shape;actin cytoskeleton organization;cellular pigment accumulation;apical protein localization
• Cellular component: cytoskeleton;microtubule;adherens junction;apical plasma membrane;cortical actin cytoskeleton;apical junction complex
• Molecular function: actin filament binding