SHROOM2

shroom family member 2, the group of PDZ domain containing|Shroom family

Basic information

Region (hg38): X:9786429-9949443

Previous symbols: [ "APXL" ]

Links

ENSG00000146950 ∙ NCBI:357 ∙ OMIM:300103 ∙ HGNC:630 ∙ Uniprot:Q13796 ∙ 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 SHROOM2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SHROOM2 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				13	10	23
missense		1	74	21	14	110
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			7	2	1	10
Total	0	1	81	36	25

Variants in SHROOM2

This is a list of pathogenic ClinVar variants found in the SHROOM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-9786555-G-A		not specified	Uncertain significance (May 20, 2024)
X-9786562-C-T		not specified	Uncertain significance (Sep 19, 2022)
X-9786618-C-A		not specified	Uncertain significance (Jul 20, 2021)
X-9786645-G-T		not specified	Uncertain significance (Oct 25, 2024)
X-9786709-A-G		not specified	Uncertain significance (Mar 22, 2023)
X-9873674-C-T		not specified	Uncertain significance (Oct 06, 2021)
X-9873708-C-T		SHROOM2-related disorder	Likely benign (Apr 15, 2019)
X-9873719-A-G		not specified	Uncertain significance (Aug 05, 2024)
X-9873752-C-T		not specified	Uncertain significance (Sep 29, 2023)
X-9891010-G-T		not specified	Uncertain significance (Aug 10, 2021)
X-9891044-C-A		not specified	Uncertain significance (May 05, 2023)
X-9891049-G-A			Likely benign (Jul 01, 2022)
X-9891058-A-G		SHROOM2-related disorder	Benign (Jul 29, 2024)
X-9891068-A-G		SHROOM2-related disorder	Benign (Dec 16, 2019)
X-9891070-C-T		SHROOM2-related disorder	Benign (Mar 20, 2019)
X-9891075-G-A		not specified	Uncertain significance (Nov 24, 2024)
X-9891092-G-A		not specified	Likely benign (Apr 13, 2022)
X-9894391-G-A		SHROOM2-related disorder	Benign (May 28, 2019)
X-9894440-G-A		not specified	Uncertain significance (Sep 08, 2024)
X-9894474-C-T		not specified	Uncertain significance (Aug 14, 2024)
X-9894524-C-T		not specified	Uncertain significance (Jan 09, 2024)
X-9894525-G-T		not specified	Uncertain significance (Jun 27, 2022)
X-9894527-G-A		not specified	Uncertain significance (Feb 15, 2023)
X-9894539-G-A		Meniere disease	Likely pathogenic (Jun 21, 2021)
X-9894590-G-A		not specified	Uncertain significance (Oct 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SHROOM2	protein_coding	protein_coding	ENST00000380913	10	162988

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00294	0.997	125715	12	20	125747	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.325	710	686	1.03	0.0000640	10382
Missense in Polyphen		212	230.97	0.91786		3531
Synonymous	-1.26	347	319	1.09	0.0000320	3426
Loss of Function	3.70	11	34.5	0.319	0.00000258	611

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000785	0.000747
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000655	0.0000462
European (Non-Finnish)	0.0000891	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.000268	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in endothelial cell morphology changes during cell spreading. In the retinal pigment epithelium, may regulate the biogenesis of melanosomes and promote their association with the apical cell surface by inducing gamma-tubulin redistribution (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.139

Intolerance Scores

• loftool: 0.446
• rvis_EVS: 1.53
• rvis_percentile_EVS: 95.54

Haploinsufficiency Scores

• pHI: 0.135
• hipred: N
• hipred_score: 0.353
• ghis: 0.406

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0858

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Shroom2

Gene ontology

• Biological process: cell morphogenesis;lens morphogenesis in camera-type eye;actin filament organization;brain development;eye pigment granule organization;cell migration;actin cytoskeleton organization;establishment of melanosome localization;melanosome organization;sodium ion transmembrane transport;camera-type eye development;cellular pigment accumulation;ear development;apical protein localization;camera-type eye morphogenesis;actin filament bundle assembly
• Cellular component: cytoskeleton;microtubule;plasma membrane;adherens junction;cell-cell adherens junction;bicellular tight junction;apical plasma membrane;cortical actin cytoskeleton;apical junction complex;extracellular exosome
• Molecular function: actin binding;protein binding;beta-catenin binding;ligand-gated sodium channel activity;actin filament binding