DYM p.Ala92=
c.276A>G · rs200169598 · VCV1168394
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.182%, mid)
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 0.6 | GERP 0.97, phastCons 1 |
| Overall | ||
| CADD | 10.94 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.182%
Middle Eastern · 11/6,038 alleles
Filtering AF
0.102%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.079%
Overall
0.0137%
220/1,611,600 alleles · rare
exomes 199/1,459,262 · genomes 21/152,338 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.182% | 549 |
| Admixed American | 0.0617% | 1,622 |
| Remaining individualsnot grpmax-eligible | 0.024% | 4,162 |
| European (non-Finnish) | 0.0122% | 8,180 |
| South Asian | 0.00769% | 13,004 |
| African / African-American | 0.00667% | 15,002 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,566 |
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
- DYM
- Protein
- p.Ala92=
- Coding
- c.276A>G
- MANE Select
- NM_001353214
- dbSNP
- rs200169598
- Type
- single nucleotide variant
- Location
- chr18:49379676 (GRCh38)
- Gene constraint
- LOEUF 1.081 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 87.91
Similar variants
- DYM c.1728+2T>C Pathogenic/Likely pathogenic ★★ same type
- DYM c.947-2A>G Pathogenic/Likely pathogenic ★★ same type
- DYM p.Arg204Ter Pathogenic ★★ same type
- DYM p.Arg428Ter Pathogenic/Likely pathogenic ★★ same type
- DYM p.Arg588Ter Pathogenic ★★ same type
- DYM p.Arg70Ter Pathogenic/Likely pathogenic ★★ same type
- DYM p.Gln306Ter Pathogenic/Likely pathogenic ★★ same type
- DYM p.Glu87Lys 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/dym-p-ala92 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown