MTMR1

myotubularin related protein 1, the group of Myotubularins|Phosphoinositide phosphatases

Basic information

Region (hg38): X:150692971-150765108

Links

ENSG00000063601 ∙ NCBI:8776 ∙ OMIM:300171 ∙ HGNC:7449 ∙ Uniprot:Q13613 ∙ 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 MTMR1 gene.

• not_specified (49 variants)
• not_provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MTMR1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001306144.3. 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				2		2
missense			48	2		50
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	48	4	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MTMR1	protein_coding	protein_coding	ENST00000544228	15	72142

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00240	123989	0	2	123991	0.00000807

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.02	150	238	0.631	0.0000189	4364
Missense in Polyphen		23	64.083	0.35891		1054
Synonymous	0.00586	94	94.1	0.999	0.00000805	1280
Loss of Function	4.41	2	26.5	0.0755	0.00000223	420

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000628	0.0000462
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.0000566	0.0000345
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Lipid phosphatase that has high specificity for phosphatidylinositol 3-phosphate and has no activity with phosphatidylinositol 4-phosphate, phosphatidylinositol (4,5)- bisphosphate and phosphatidylinositol (3,4,5)-trisphosphate (PubMed:11733541, PubMed:27018598). Activity with phosphatidylinositol (3,5)-bisphosphate is controversial; it has been shown by PubMed:27018598, while PubMed:11733541 find no activity with this substrate. {ECO:0000269|PubMed:11733541, ECO:0000269|PubMed:27018598}.
• Pathway: Inositol phosphate metabolism - Homo sapiens (human);Phosphatidylinositol signaling system - Homo sapiens (human);Metabolism of lipids;Metabolism;Nicotinate Nicotinamide metabolism;Synthesis of PIPs at the plasma membrane;PI Metabolism;Phospholipid metabolism (Consensus)

Recessive Scores

• pRec: 0.176

Intolerance Scores

• loftool: 0.175
• rvis_EVS: -0.09
• rvis_percentile_EVS: 46.74

Haploinsufficiency Scores

• pHI: 0.400
• hipred: Y
• hipred_score: 0.696
• ghis: 0.520

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.469

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mtmr1
• Phenotype: normal phenotype

Gene ontology

• Biological process: phosphatidylinositol biosynthetic process;peptidyl-tyrosine dephosphorylation;phosphatidylinositol dephosphorylation;regulation of phosphatidylinositol dephosphorylation
• Cellular component: cytoplasm;cytosol;plasma membrane
• Molecular function: phosphatidylinositol-3-phosphatase activity;protein tyrosine phosphatase activity;protein homodimerization activity;phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity