DYM p.Leu580=
c.1740A>G · rs549366750 · VCV1638449
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.005%, 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 -0.77 | GERP -5, phastCons 0.006 |
| Overall | ||
| CADD | 5.266 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.005%
Admixed American · 3/60,016 alleles
Filtering AF
0.00133%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000668%
Overall
0.00031%
5/1,614,042 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.005% | 20,005 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,243 |
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.Leu580=
- Coding
- c.1740A>G
- MANE Select
- NM_001353214
- dbSNP
- rs549366750
- Type
- single nucleotide variant
- Location
- chr18:49118915 (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-leu580 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown