DYM p.Leu53=
c.159G>A · rs774446496 · VCV1627598
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.01%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.72 | GERP 0.9, phastCons 1 |
| Overall | ||
| CADD | 13.08 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.01%
Admixed American · 6/59,958 alleles
Filtering AF
0.00429%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00295%
Overall
0.00093%
15/1,613,184 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.01% | 9,993 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,442 |
| European (non-Finnish) | 0.000678% | 147,445 |
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.Leu53=
- Coding
- c.159G>A
- MANE Select
- NM_001353214
- dbSNP
- rs774446496
- Type
- single nucleotide variant
- Location
- chr18:49391627 (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 p.Leu53Val Uncertain significance ★ ⚠ same residue
- 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
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-leu53 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown