DYSF p.Asp1491=
c.4473C>T · rs948317553 · VCV513723
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0202%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>G here scores Δ0.43 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -8.1 | GERP -4.1 |
| Overall | ||
| CADD | 7.694 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0202%
South Asian · 17/84,062 alleles
Filtering AF
0.0129%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0105%
Overall
0.00464%
72/1,551,660 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0202% | 4,945 |
| Remaining individualsnot grpmax-eligible | 0.0133% | 7,514 |
| African / African-American | 0.00957% | 10,450 |
| East Asian | 0.00489% | 20,452 |
| European (non-Finnish) | 0.00331% | 30,184 |
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
- DYSF
- Protein
- p.Asp1491=
- Coding
- c.4473C>T
- MANE Select
- NM_001130987
- dbSNP
- rs948317553
- Type
- single nucleotide variant
- Location
- chr2:71620555 (GRCh38)
- Gene constraint
- LOEUF 0.836 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.25 · 11 PDB
Similar variants
- DYSF c.1003-3C>A Pathogenic ★★★ same type
- DYSF c.1033+1G>A Pathogenic ★★★ same type
- DYSF c.1033+4A>T Likely pathogenic ★★★ same type
- DYSF c.1033+5G>A Likely pathogenic ★★★ same type
- DYSF c.1149+1G>A Pathogenic ★★★ same type
- DYSF c.1149+1G>C Pathogenic ★★★ same type
- DYSF c.1149+4A>G Pathogenic ★★★ same type
- DYSF c.1149+5G>A 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/dysf-p-asp1491 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown