MTM1 p.Asn331=
c.993T>C · VCV4953203
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00177%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.43 | GERP -4, phastCons 0.15 |
| Overall | ||
| CADD | 4.099 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00177%
South Asian · 1/56,607 alleles
Overall
8.26e-05%
1/1,209,971 alleles · very rare
exomes 1/1,095,949 · genomes 0/114,022 · joint denominator
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
- MTM1
- Protein
- p.Asn331=
- Coding
- c.993T>C
- MANE Select
- NM_000252
- Type
- single nucleotide variant
- Location
- chrX:150649841 (GRCh38)
- Structure
- AlphaFold pLDDT 90.10
- Residue 331
- the myotubularin phosphatase domain
Similar variants
- MTM1 c.1644+1G>A Pathogenic ★★★ same type
- MTM1 p.Arg224Ter Pathogenic ★★★ same type
- MTM1 p.Arg69Cys Pathogenic ★★★ same type
- MTM1 p.Gln451= Likely pathogenic ★★★ same type
- MTM1 p.Glu404Lys Pathogenic ★★★ same type
- MTM1 p.Pro205Leu Pathogenic ★★★ same type
- MTM1 p.Trp230Arg Likely pathogenic ★★★ same type
- MTM1 p.Trp230Cys Likely pathogenic ★★★ 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/mtm1-p-asn331 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown