MYSM1 p.Asp244=
c.732T>C · rs1644757769 · VCV1923317
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
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 1.4 | GERP 1.2 |
| Overall | ||
| CADD | 1.27 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/59,920 alleles
Overall
0.000124%
2/1,613,158 alleles · very rare
exomes 0/1,460,938 · genomes 2/152,220 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00167% | 59,920 |
| African / African-American | 0.00134% | 74,906 |
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.Asp244=
- Coding
- c.732T>C
- MANE Select
- NM_001085487
- dbSNP
- rs1644757769
- Type
- single nucleotide variant
- Location
- chr1:58682312 (GRCh38)
- Gene constraint
- LOEUF 0.578 · pLI 0.09 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 64.69 · 2 PDB
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-asp244 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown