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.

• not_specified (120 variants)
• MTMR7-related_disorder (5 variants)

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. These statistics are base on transcript: NM_000004686.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			119	4		123
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	119	5	0

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