MTM1 p.Arg62=
c.186A>G · VCV4953200
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.44 | acceptor loss · deltas |
|---|---|---|
| Pangolin | Δ0.40 | loss · gain 0.00 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 9.2 | GERP 2.2, phastCons 1 |
| Overall | ||
| CADD | 13.39 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- MTM1
- Protein
- p.Arg62=
- Coding
- c.186A>G
- MANE Select
- NM_000252
- Type
- single nucleotide variant
- Location
- chrX:150598641 (GRCh38)
- Structure
- AlphaFold pLDDT 90.10
- Residue 62
- the gram 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-arg62 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown