SHROOM1

shroom family member 1, the group of Shroom family

Basic information

Region (hg38): 5:132822140-132830659

Links

ENSG00000164403 ∙ NCBI:134549 ∙ OMIM:611179 ∙ HGNC:24084 ∙ Uniprot:Q2M3G4 ∙ 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 SHROOM1 gene.

• Inborn genetic diseases (36 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SHROOM1 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				2	1	3
missense			35	2		37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	35	4	1

Variants in SHROOM1

This is a list of pathogenic ClinVar variants found in the SHROOM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-132822857-G-C		not specified	Uncertain significance (Mar 06, 2023)
5-132822876-G-A		not specified	Uncertain significance (Dec 28, 2022)
5-132822900-C-A		not specified	Uncertain significance (May 15, 2023)
5-132822930-G-A		not specified	Uncertain significance (Feb 28, 2024)
5-132823278-G-T		not specified	Uncertain significance (Feb 15, 2023)
5-132823287-A-T		not specified	Uncertain significance (Dec 02, 2021)
5-132823360-T-A		not specified	Uncertain significance (Apr 22, 2022)
5-132823410-G-A		not specified	Uncertain significance (Aug 23, 2021)
5-132823483-G-A		not specified	Uncertain significance (Mar 07, 2024)
5-132823507-G-A		not specified	Uncertain significance (Dec 13, 2023)
5-132823631-C-T		not specified	Uncertain significance (Dec 16, 2021)
5-132823883-G-A		not specified	Uncertain significance (Nov 23, 2021)
5-132823884-C-T			Benign/Likely benign (Dec 01, 2022)
5-132823889-C-A		not specified	Uncertain significance (Oct 13, 2023)
5-132823899-G-C		not specified	Uncertain significance (May 31, 2023)
5-132823899-G-T		not specified	Uncertain significance (Jun 28, 2022)
5-132824094-C-T		not specified	Uncertain significance (May 23, 2023)
5-132824109-G-A		not specified	Uncertain significance (Mar 12, 2024)
5-132824184-T-G		not specified	Uncertain significance (Apr 17, 2023)
5-132824205-C-T		not specified	Uncertain significance (Aug 20, 2023)
5-132824286-C-T		not specified	Uncertain significance (May 24, 2023)
5-132824298-G-T		not specified	Uncertain significance (Sep 16, 2021)
5-132824342-G-A		SHROOM1-related disorder • not specified	Conflicting classifications of pathogenicity (Sep 29, 2023)
5-132824388-C-T		not specified	Uncertain significance (Mar 21, 2023)
5-132824705-G-T		not specified	Uncertain significance (Nov 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SHROOM1	protein_coding	protein_coding	ENST00000378679	7	8758

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0457	0.954	125694	0	29	125723	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.923	397	452	0.878	0.0000264	5268
Missense in Polyphen		99	120.62	0.82077		1537
Synonymous	1.99	165	201	0.821	0.0000123	1947
Loss of Function	3.25	7	24.3	0.288	0.00000110	296

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000250	0.000238
Ashkenazi Jewish	0.00101	0.000993
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000882	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in the assembly of microtubule arrays during cell elongation. {ECO:0000250}.

Recessive Scores

• pRec: 0.0887

Intolerance Scores

• loftool: 0.779
• rvis_EVS: -1.24
• rvis_percentile_EVS: 5.41

Haploinsufficiency Scores

• pHI: 0.0950
• hipred: N
• hipred_score: 0.357
• ghis: 0.512

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0855

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Shroom1

Gene ontology

• Biological process: cell morphogenesis;actin filament organization;actin cytoskeleton organization;actin filament bundle assembly
• Cellular component: microtubule;adherens junction;apical plasma membrane;cortical actin cytoskeleton;apical junction complex
• Molecular function: myosin II binding;actin filament binding