MTMR3 p.Phe292=
c.876C>T · rs146523702 · VCV2653054
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.967%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1 | GERP -5.3, phastCons 0.003 |
| Overall | ||
| CADD | 13.06 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.967%
African / African-American · 726/75,054 alleles
Filtering AF
0.909%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.886%
Overall
0.0548%
885/1,613,910 alleles · rare
exomes 474/1,461,580 · genomes 411/152,330 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.967% | 103 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0642% | 1,558 |
| Remaining individualsnot grpmax-eligible | 0.0624% | 1,603 |
| Admixed American | 0.0217% | 4,616 |
| European (non-Finnish) | 0.00737% | 13,563 |
| South Asian | 0.0011% | 91,066 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- MTMR3
- Protein
- p.Phe292=
- Coding
- c.876C>T
- MANE Select
- NM_021090
- dbSNP
- rs146523702
- Type
- single nucleotide variant
- Location
- chr22:30007318 (GRCh38)
- Gene constraint
- LOEUF 0.302 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 66.94
- Residue 292
- the myotubularin phosphatase domain
Similar variants
- MTMR3 p.Ala117Pro Uncertain significance ★ ⚠ same type
- MTMR3 p.Arg177Lys Uncertain significance ★ ⚠ same type
- MTMR3 p.Arg266Leu Uncertain significance ★ ⚠ same type
- MTMR3 p.Arg275Ser Uncertain significance ★ ⚠ same type
- MTMR3 p.Arg47Leu Uncertain significance ★ same type
- MTMR3 p.Arg6Trp Uncertain significance ★ ⚠ same type
- MTMR3 p.Asn116Ser Uncertain significance ★ ⚠ same type
- MTMR3 p.Asn283Ser Uncertain significance ★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/mtmr3-p-phe292 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown