MTMR7

myotubularin related protein 7, the group of Myotubularins|Phosphoinositide phosphatases

Basic information

Region (hg38): 8:17296794-17413528

Links

ENSG00000003987 ∙ NCBI:9108 ∙ OMIM:603562 ∙ HGNC:7454 ∙ Uniprot:Q9Y216 ∙ 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 MTMR7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MTMR7 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				1		1
missense			52	3		55
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	52	4	1

Variants in MTMR7

This is a list of pathogenic ClinVar variants found in the MTMR7 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-17299879-C-G		not specified	Uncertain significance (Aug 12, 2022)
8-17299900-C-A		not specified	Uncertain significance (Aug 08, 2023)
8-17299914-T-G		not specified	Uncertain significance (Mar 02, 2023)
8-17299947-C-G		not specified	Uncertain significance (May 06, 2022)
8-17299948-G-A		not specified	Uncertain significance (Nov 09, 2023)
8-17299950-C-G		not specified	Uncertain significance (Jun 16, 2024)
8-17300022-T-C		not specified	Uncertain significance (Mar 16, 2024)
8-17300094-C-A		not specified	Uncertain significance (Oct 14, 2023)
8-17300094-C-T		not specified	Uncertain significance (Jan 17, 2024)
8-17300096-A-C		MTMR7-related disorder	Likely benign (Nov 29, 2022)
8-17300109-G-T		not specified	Uncertain significance (Nov 08, 2022)
8-17300181-A-G		not specified	Uncertain significance (Dec 03, 2021)
8-17300215-T-C		not specified	Uncertain significance (Nov 02, 2023)
8-17302159-C-G		not specified	Uncertain significance (Aug 28, 2023)
8-17302170-A-C		not specified	Uncertain significance (Feb 14, 2023)
8-17302204-C-T		not specified	Uncertain significance (Mar 23, 2023)
8-17302209-A-G		MTMR7-related disorder	Likely benign (Feb 03, 2022)
8-17302238-C-A		not specified	Uncertain significance (Nov 09, 2023)
8-17302258-G-A		not specified	Uncertain significance (Jun 24, 2022)
8-17304385-A-G		not specified	Uncertain significance (Aug 01, 2022)
8-17304412-T-G		not specified	Uncertain significance (May 26, 2024)
8-17304461-G-C		not specified	Uncertain significance (Feb 27, 2023)
8-17305784-T-C		not specified	Uncertain significance (Apr 19, 2024)
8-17305850-T-C		not specified	Uncertain significance (Nov 19, 2022)
8-17305913-A-G		not specified	Uncertain significance (May 03, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MTMR7	protein_coding	protein_coding	ENST00000180173	14	115499

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.21e-14	0.597	125685	1	62	125748	0.000251

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.61	465	377	1.23	0.0000213	4378
Missense in Polyphen		168	160	1.05		1916
Synonymous	-2.71	179	138	1.29	0.00000797	1201
Loss of Function	1.64	27	37.9	0.712	0.00000213	419

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000388	0.000388
Ashkenazi Jewish	0.00	0.00
East Asian	0.000219	0.000217
Finnish	0.000697	0.000647
European (Non-Finnish)	0.000282	0.000281
Middle Eastern	0.000219	0.000217
South Asian	0.0000653	0.0000653
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Phosphatase that acts on lipids with a phosphoinositol headgroup. {ECO:0000305}.
• Pathway: Inositol phosphate metabolism - Homo sapiens (human);Phosphatidylinositol signaling system - Homo sapiens (human);Metabolism of lipids;Metabolism;Inositol phosphate metabolism;Synthesis of PIPs at the late endosome membrane;PI Metabolism;Phospholipid metabolism;Synthesis of IP2, IP, and Ins in the cytosol (Consensus)

Recessive Scores

• pRec: 0.121

Intolerance Scores

• loftool: 0.171
• rvis_EVS: -1.13
• rvis_percentile_EVS: 6.56

Haploinsufficiency Scores

• pHI: 0.181
• hipred: N
• hipred_score: 0.445
• ghis: 0.591

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.404

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mtmr7

Gene ontology

• Biological process: protein dephosphorylation;phosphatidylinositol biosynthetic process;peptidyl-tyrosine dephosphorylation;inositol phosphate dephosphorylation;phosphatidylinositol dephosphorylation
• Cellular component: cytoplasm;cytosol;membrane
• Molecular function: phosphatidylinositol-3-phosphatase activity;protein tyrosine phosphatase activity;protein binding;phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity