MYSM1 p.Pro665=
c.1995T>G · VCV3649777
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.48e-05%, nfe)
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 0.075 | GERP -0.72, phastCons 0.1 |
| Overall | ||
| CADD | 7.639 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.48e-05%
European (non-Finnish) · 1/1,179,102 alleles
Overall
6.2e-05%
1/1,612,504 alleles · very rare
exomes 1/1,460,368 · genomes 0/152,136 · 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
- MYSM1
- Protein
- p.Pro665=
- Coding
- c.1995T>G
- MANE Select
- NM_001085487
- Type
- single nucleotide variant
- Location
- chr1:58667074 (GRCh38)
- Gene constraint
- LOEUF 0.578 · pLI 0.09 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 64.69 · 2 PDB
- Residue 665
- a UniProt-annotated variant site (in bmfs4); the mpn domain
Similar variants
- MYSM1 p.Arg506Ter Pathogenic ★★ same type
- MYSM1 p.Gln629Ter Pathogenic ★★ same type
- MYSM1 p.Arg138Gln Uncertain significance ★★ ⚠ same type
- MYSM1 p.Arg150Cys Uncertain significance ★★ ⚠ same type
- MYSM1 p.Arg204Cys Uncertain significance ★★ ⚠ same type
- MYSM1 p.Arg478Gln Uncertain significance ★★ ⚠ same type
- MYSM1 p.Arg494His Uncertain significance ★★ ⚠ same type
- MYSM1 p.Arg499His 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/mysm1-p-pro665 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown