DRP2 p.Ser889=
c.2667G>A · rs749273269 · VCV1936635
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00881%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.78 | acceptor gain · deltas |
|---|---|---|
| Pangolin | Δ0.57 | gain · loss 0.37 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP -2.4 | GERP -2.9 |
| Overall | ||
| CADD | 16.67 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00881%
South Asian · 5/56,737 alleles
Filtering AF
0.00341%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00217%
Overall
0.000744%
9/1,209,328 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00881% | 11,347 |
| Admixed American | 0.00437% | 22,861 |
| African / African-American | 0.00176% | 56,890 |
| European (non-Finnish) | 0.000112% | 895,087 |
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
- DRP2
- Protein
- p.Ser889=
- Coding
- c.2667G>A
- MANE Select
- NM_001197293 · reported on NM_001939
- dbSNP
- rs749273269
- Type
- single nucleotide variant
- Location
- chrX:101260087 (GRCh38)
- Structure
- AlphaFold pLDDT 90.49 · 15 PDB
Similar variants
- DRP2 p.Ser889Leu Uncertain significance ★★ ⚠ 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/drp2-p-ser889 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown