MTMR6
protein-codingmyotubularin related protein 6, the group of Myotubularins|Phosphoinositide phosphatases
Gene summary
Enables phosphatidylinositol-3,5-bisphosphate phosphatase activity and phosphatidylinositol-3-phosphate phosphatase activity. Involved in phosphatidylinositol dephosphorylation. Located in cytoplasm and nuclear envelope. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~41.3 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 MTMR6 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_004685.5. 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 | 76 | 6 | 82 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 79 | 6 | 0 | 85 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_004676.3 | 14 | MANE Select | |
| Ensembl | ENSP00000371221.5 | 14 | MANE Select | |
| RefSeq | NP_001372159.1 | 15 | Standard | |
| RefSeq | NP_001372160.1 | 14 | 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
- protein dephosphorylation
- phosphatidylinositol biosynthetic process
- peptidyl-tyrosine dephosphorylation
- phosphatidylinositol dephosphorylation
- potassium ion transmembrane transport
Molecular Function
- phosphatidylinositol-3-phosphatase activity
- protein serine/threonine phosphatase activity
- protein tyrosine phosphatase activity
- protein binding
- calcium-activated potassium channel activity
Cellular Component
- nuclear envelope
- cytoplasm
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000381801
- Coding exons
- 14
- Length
- 59841
- Individuals with no LoFs
- 125708
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 40
- Defined
- 125748
- p
- 0.000159
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.871 | 276 | 320 | 0.863 | 0.0000157 | 4104 |
| Missense (PolyPhen) | 63 | 110.27 | 0.57132 | 1405 | ||
| Synonymous | 0.910 | 102 | 114 | 0.892 | 0.00000571 | 1097 |
| Loss of Function | 2.70 | 18 | 35.3 | 0.510 | 0.00000185 | 427 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00031 | 0.00031 | rare |
| Latino/Admixed American | 0.000089 | 0.000087 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000055 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00024 | 0.00024 | rare |
| South Asian | 0.00014 | 0.00013 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Phosphatase that acts on lipids with a phosphoinositol headgroup. Acts as a negative regulator of KCNN4/KCa3.1 channel activity in CD4+ T-cells possibly by decreasing intracellular levels of phosphatidylinositol 3 phosphatase. Negatively regulates proliferation of reactivated CD4+ T-cells. {ECO:0000269|PubMed:15831468, ECO:0000269|PubMed:16847315}.;
Recessive Scores
- pRec
- 0.157
Intolerance Scores
- LoFtool
- 0.247
- RVIS EVS
- 0.95
- RVIS percentile EVS
- 90.09
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.989
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | High | Medium | High |
| Cancer | High | Medium | High |