MTMR7
protein-codingmyotubularin related protein 7, the group of Myotubularins|Phosphoinositide phosphatases
Gene summary
This gene encodes a member of the myotubularin family of tyrosine/dual-specificity phosphatases. The encoded protein is characterized by four distinct domains that are conserved among all members of the myotubularin family: the glucosyltransferase, Rab-like GTPase activator and myotubularins domain, the Rac-induced recruitment domain, the protein tyrosine phosphatases and dual-specificity phosphatases domain and the suppressor of variegation 3-9, enhancer-of-zeste, and trithorax interaction domain. This protein dephosphorylates the target substrates phosphatidylinositol 3-phosphate and inositol 1,3-bisphosphate. A pseudogene of this gene is found on chromosome 5. [provided by RefSeq, Mar 2009]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~116.7 kbGenCC 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 MTMR7 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_004686.5. 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 | 1 | 1 | ||||
| missense | 135 | 4 | 139 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 135 | 5 | 0 | 140 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_004677.3 | 14 | MANE Select | |
| Ensembl | ENSP00000180173.4 | 14 | MANE Select | |
| Ensembl | ENSP00000431000.1 | 4 | Standard | |
| Ensembl | ENSP00000429733.1 | 13 | 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
- Inositol phosphate metabolism
Biological Process
- protein dephosphorylation
- phosphatidylinositol biosynthetic process
- peptidyl-tyrosine dephosphorylation
- inositol phosphate dephosphorylation
- phosphatidylinositol dephosphorylation
Molecular Function
- phosphatidylinositol-3-phosphatase activity
- protein tyrosine phosphatase activity
- protein binding
- phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity
Cellular Component
- cytoplasm
- cytosol
- membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000180173
- Coding exons
- 14
- Length
- 115499
- Individuals with no LoFs
- 125685
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 62
- Defined
- 125748
- p
- 0.000251
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -1.61 | 465 | 377 | 1.23 | 0.0000213 | 4378 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00018 | 0.00018 | rare |
| Latino/Admixed American | 0.00020 | 0.00020 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00022 | 0.00022 | rare |
| Finnish | 0.00070 | 0.00065 | rare |
| European (Non-Finnish) | 0.00028 | 0.00028 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0.00017 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Phosphatase that acts on lipids with a phosphoinositol headgroup. {ECO:0000305}.;
Recessive Scores
- pRec
- 0.121
Intolerance Scores
- LoFtool
- 0.171
- RVIS EVS
- -1.13
- RVIS percentile EVS
- 6.56
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.404
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |