MTSS1

MTSS I-BAR domain containing 1, the group of I-BAR domain containing

Basic information

Region (hg38): 8:124550784-124728473

Links

ENSG00000170873 ∙ NCBI:9788 ∙ OMIM:608486 ∙ HGNC:20443 ∙ Uniprot:O43312 ∙ 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 MTSS1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MTSS1 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			47			47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	2
Total	0	0	47	2	3

Variants in MTSS1

This is a list of pathogenic ClinVar variants found in the MTSS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-124553018-C-T		not specified	Uncertain significance (Mar 15, 2024)
8-124553120-C-G		not specified	Uncertain significance (May 02, 2024)
8-124553132-C-T		not specified	Uncertain significance (Feb 27, 2024)
8-124553161-C-G		not specified	Uncertain significance (Sep 17, 2021)
8-124553176-G-C		not specified	Uncertain significance (Jul 20, 2021)
8-124553195-C-T		not specified	Uncertain significance (Feb 21, 2024)
8-124553261-C-T		not specified	Uncertain significance (May 31, 2023)
8-124553267-A-C		not specified	Uncertain significance (May 03, 2023)
8-124553317-G-A		not specified	Uncertain significance (Aug 29, 2023)
8-124553336-C-T		not specified	Uncertain significance (Apr 19, 2024)
8-124553338-C-T		not specified	Uncertain significance (May 25, 2022)
8-124553339-C-T		not specified	Uncertain significance (Dec 08, 2023)
8-124553342-G-A		not specified	Uncertain significance (Aug 12, 2022)
8-124553366-C-G		not specified	Uncertain significance (Feb 05, 2024)
8-124553402-T-C		not specified	Uncertain significance (Apr 24, 2024)
8-124553423-T-C		not specified	Uncertain significance (Jun 13, 2022)
8-124553518-A-G		not specified	Uncertain significance (Aug 30, 2021)
8-124553527-C-T		not specified	Uncertain significance (Dec 03, 2021)
8-124553563-C-T		not specified	Uncertain significance (Oct 26, 2022)
8-124553570-C-T		not specified	Uncertain significance (May 09, 2022)
8-124555780-G-A		not specified	Uncertain significance (Apr 08, 2022)
8-124555823-G-A		not specified	Uncertain significance (Sep 01, 2021)
8-124555832-T-C		not specified	Uncertain significance (Jun 29, 2022)
8-124555852-C-T		not specified	Uncertain significance (Jan 18, 2023)
8-124555873-A-C		not specified	Uncertain significance (Aug 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MTSS1	protein_coding	protein_coding	ENST00000518547	14	177700

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000296	125744	0	2	125746	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.81	348	457	0.761	0.0000273	4890
Missense in Polyphen		141	219.9	0.6412		2257
Synonymous	0.989	159	176	0.905	0.0000108	1538
Loss of Function	5.14	3	36.5	0.0822	0.00000198	400

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000917	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be related to cancer progression or tumor metastasis in a variety of organ sites, most likely through an interaction with the actin cytoskeleton.
• Pathway: HH-Ncore;EGF-Ncore;Hedgehog signaling events mediated by Gli proteins (Consensus)

Recessive Scores

• pRec: 0.999

Intolerance Scores

• loftool: 0.0290
• rvis_EVS: -0.82
• rvis_percentile_EVS: 11.94

Haploinsufficiency Scores

• pHI: 0.371
• hipred: Y
• hipred_score: 0.725
• ghis: 0.498

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.976

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mtss1
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; immune system phenotype; skeleton phenotype; renal/urinary 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); hematopoietic system phenotype; neoplasm

Gene ontology

• Biological process: plasma membrane organization;cell adhesion;transmembrane receptor protein tyrosine kinase signaling pathway;microspike assembly;actin cytoskeleton organization;negative regulation of epithelial cell proliferation;renal tubule morphogenesis;cellular response to fluid shear stress;glomerulus morphogenesis;nephron tubule epithelial cell differentiation;epithelial cell proliferation involved in renal tubule morphogenesis
• Cellular component: ruffle;cytoplasm;actin cytoskeleton;endocytic vesicle
• Molecular function: actin monomer binding;signaling receptor binding;protein binding;identical protein binding