DYM p.Ile8=
c.24C>T · rs759732045 · VCV2897310
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0164%, mid)
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 -1.3 | GERP -3.4 |
| Overall | ||
| CADD | 1.073 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0164%
Middle Eastern · 1/6,082 alleles
Filtering AF
0.00359%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00255%
Overall
0.0018%
29/1,613,636 alleles · ultra-rare
exomes 26/1,461,562 · genomes 3/152,074 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0164% | 6,082 |
| South Asian | 0.00769% | 13,012 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,240 |
| Admixed American | 0.00167% | 59,984 |
| European (non-Finnish) | 0.00153% | 65,554 |
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.Ile8=
- Coding
- c.24C>T
- MANE Select
- NM_001353214
- dbSNP
- rs759732045
- Type
- single nucleotide variant
- Location
- chr18:49430371 (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-ile8 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown