MTM1 p.Phe438fs
c.1306_1310dup · rs398123267 · VCV92670
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 12 of 15 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 7.7 | GERP 2.2, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- MTM1
- Protein
- p.Phe438fs
- Coding
- c.1306_1310dup
- MANE Select
- NM_000252
- dbSNP
- rs398123267
- Type
- Duplication
- Location
- chrX:150659707 (GRCh38)
- Structure
- AlphaFold pLDDT 90.10
- Residue 438
- the myotubularin phosphatase domain
Similar variants
- MTM1 p.Arg184fs Pathogenic ★★ same type
- MTM1 p.Gly177fs Pathogenic ★★ same type
- MTM1 p.Met317fs Pathogenic ★★ same type
- MTM1 p.Tyr198Ter Pathogenic ★★ same type
- MTM1 p.Val324fs Pathogenic ★★ same type
- MTM1 c.137-11dup Benign/Likely benign ★★ same type
- MTM1 c.867_867+1dup Pathogenic ★ same type
- MTM1 p.Asp25fs 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-phe438fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown