MTMR9
protein-codingmyotubularin related protein 9, the group of Myotubularins
Gene summary
This gene encodes a myotubularin-related protein that is atypical to most other members of the myotubularin-related protein family because it has no dual-specificity phosphatase domain. The encoded protein contains a double-helical motif similar to the SET interaction domain, which is thought to have a role in the control of cell proliferation. In mouse, a protein similar to the encoded protein binds with MTMR7, and together they dephosphorylate phosphatidylinositol 3-phosphate and inositol 1,3-bisphosphate. [provided by RefSeq, Jul 2008]
- C8orf9
- MTMR8
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~43.3 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 MTMR9 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_015458.4. 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 | 120 | 4 | 2 | 126 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 122 | 4 | 3 | 129 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_056273.2 | 10 | MANE Select | |
| Ensembl | ENSP00000221086.3 | 10 | MANE Select | |
| Ensembl | ENSP00000433239.1 | 9 | Standard | |
| Ensembl | ENSP00000433239.1 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Metabolism of lipids
- Metabolism
- Inositol phosphate metabolism
- Synthesis of PIPs at the plasma membrane
- Synthesis of PIPs at the late endosome membrane
Biological Process
- phosphatidylinositol biosynthetic process
- negative regulation of autophagy
- positive regulation of phosphatase activity
- dephosphorylation
- protein stabilization
Molecular Function
- phosphatidylinositol-3-phosphatase activity
- protein binding
- protein phosphatase binding
- enzyme regulator activity
- phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity
Cellular Component
- cytoplasm
- cytosol
- protein-containing complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000221086
- Coding exons
- 10
- Length
- 43722
- Individuals with no LoFs
- 125732
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 16
- Defined
- 125748
- p
- 0.0000636
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -2.33 | 418 | 304 | 1.38 | 0.0000157 | 3605 |
| Missense (PolyPhen) | 80 | 86.318 | 0.9268 | 990 | ||
| Synonymous | -4.01 | 167 | 113 | 1.48 | 0.00000586 | 1035 |
| Loss of Function | 3.46 | 11 | 32.2 | 0.341 | 0.00000184 | 329 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.000060 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0.000092 | 0.000092 | rare |
| European (Non-Finnish) | 0.000071 | 0.000070 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Probable pseudophosphatase. Contains a Gly residue instead of a conserved Cys residue in the dsPTPase catalytic loop which renders it catalytically inactive as a phosphatase (Potential). {ECO:0000305}.;
Recessive Scores
- pRec
- 0.114
Intolerance Scores
- LoFtool
- 0.0637
- RVIS EVS
- -0.82
- RVIS percentile EVS
- 11.94
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.882
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |