MTMR1

protein-coding

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

Gene summary

This gene encodes a member of the myotubularin related family of proteins. Members of this family contain the consensus sequence for the active site of protein tyrosine phosphatases. Alternatively spliced variants have been described but their biological validity has not been determined. [provided by RefSeq, Jul 2008]

MANE transcript

NM_001306144.3

Inheritance

—

ClinVar variants

U:168B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.08

Max pathogenic AF

—

Genomic locus

chrX:150,692,971-150,765,108

External References & Databases

Ensembl (ENSG00000063601)

Transcript & Mutation Effects

hg38 • Region Span ~72.1 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MTMR1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 52

not providedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001306144.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			23 clinvar	2 clinvar		25
missense			107 clinvar	2 clinvar		109
nonsense			17 clinvar			17
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			21 clinvar			21
Total	0	0	168	4	0	172

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 53 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001306144.3	RefSeq	NP_001293073.1	16	MANE Select
ENST00000445323.7	Ensembl	ENSP00000414178.2	16	MANE Select
NM_001306145.2	RefSeq	NP_001293074.1	10	Standard
NM_001353990.2	RefSeq	NP_001340919.1	16	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Inositol phosphate metabolism - Homo sapiens (human)
Phosphatidylinositol signaling system - Homo sapiens (human)
Metabolism of lipids
Metabolism
Nicotinate Nicotinamide metabolism

Biological Process

phosphatidylinositol biosynthetic process
peptidyl-tyrosine dephosphorylation
phosphatidylinositol dephosphorylation
regulation of phosphatidylinositol dephosphorylation

Molecular Function

phosphatidylinositol-3-phosphatase activity
protein tyrosine phosphatase activity
protein homodimerization activity
phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity

Cellular Component

cytoplasm
cytosol
plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000544228
Coding exons: 15
Length: 72142
Individuals with no LoFs: 123989
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 123991
p: 0.00000807

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.02	150	238	0.631	0.0000189	4364
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000063	0.000046	rare
European (Non-Finnish)	0	0.0	absent
South Asian	0.000057	0.000035	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.176

Intolerance Scores

LoFtool: 0.175
RVIS EVS: -0.09
RVIS percentile EVS: 46.74

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.469

Gene Damage Prediction

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