DPYSL2 p.Val65=
c.195G>A · VCV4084347
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.285%, 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 3.7 | GERP -1.4, phastCons 1 |
| Overall | ||
| CADD | 12.5 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.285%
Middle Eastern · 17/5,970 alleles
Filtering AF
0.181%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.149%
Overall
0.0017%
26/1,530,178 alleles · rare
exomes 21/1,377,894 · genomes 5/152,284 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.285% | 351 |
| Remaining individualsnot grpmax-eligible | 0.00334% | 29,904 |
| African / African-American | 0.00276% | 36,289 |
| European (non-Finnish) | 0.000437% | 228,970 |
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
- DPYSL2
- Protein
- p.Val65=
- Coding
- c.195G>A
- MANE Select
- NM_001197293
- Type
- single nucleotide variant
- Location
- chr8:26514520 (GRCh38)
- Gene constraint
- LOEUF 0.29 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 90.49 · 15 PDB
- Residue 65
- a β-strand
Similar variants
- DRP2 p.Asn65= Likely benign ★ same residue
- DRP2 p.Glu432Ter Pathogenic ★★ same type
- DPYSL2 p.Asn492Ser Uncertain significance ★★ ⚠ same type
- DPYSL2 p.Asp520Asn Uncertain significance ★★ ⚠ same type
- DRP2 p.Ala205Val Uncertain significance ★★ ⚠ same type
- DRP2 p.Ala643Thr Uncertain significance ★★ ⚠ same type
- DRP2 p.Arg199His Uncertain significance ★★ ⚠ same type
- DRP2 p.Arg224Cys Uncertain significance ★★ ⚠ 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/dpysl2-p-val65 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown