PRKDC p.Ala331=
c.993A>G · rs2551880158 · VCV1768661
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00566%, sas)
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 -1.9 | GERP -4.3 |
| Overall | ||
| CADD | 6.735 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00566%
South Asian · 5/88,300 alleles
Filtering AF
0.00215%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0014%
Overall
0.000312%
5/1,604,448 alleles · very rare
exomes 5/1,452,074 · genomes 0/152,374 · joint denominator
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
- PRKDC
- Protein
- p.Ala331=
- Coding
- c.993A>G
- MANE Select
- NM_006904
- dbSNP
- rs2551880158
- Type
- single nucleotide variant
- Location
- chr8:47939671 (GRCh38)
- Gene constraint
- LOEUF 0.183 · pLI 1.00 (gnomAD)
- Residue 331
- a turn
Similar variants
- PRKDC p.Ala331Thr Uncertain significance ★★ ⚠ same residue
- PRKDC c.2259+6C>T Uncertain significance ★★ same type
- PRKDC c.3464+4G>A Uncertain significance ★★ same type
- PRKDC c.5235+6T>C Uncertain significance ★★ same type
- PRKDC c.5919+5G>A Uncertain significance ★★ same type
- PRKDC p.Ala1008Val Uncertain significance ★★ ⚠ same type
- PRKDC p.Ala1103Val Uncertain significance ★★ ⚠ same type
- PRKDC p.Ala1130Ser 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/prkdc-p-ala331 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown