PRKD2 p.Cys306=
c.918C>T · rs74510632 · VCV711222
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.638%, afr)
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 -3.4 | GERP -3.7 |
| Overall | ||
| CADD | 6.681 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.638%
African / African-American · 479/75,046 alleles
Filtering AF
0.591%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.572%
Overall
0.0369%
596/1,614,188 alleles · rare
exomes 320/1,461,880 · genomes 276/152,308 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.638% | 157 |
| Admixed American | 0.0716% | 1,396 |
| Remaining individualsnot grpmax-eligible | 0.064% | 1,563 |
| Middle Eastern | 0.0165% | 6,062 |
| South Asian | 0.00329% | 30,361 |
| European (non-Finnish) | 0.00254% | 39,334 |
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
- PRKD2
- Protein
- p.Cys306=
- Coding
- c.918C>T
- MANE Select
- NM_016457
- dbSNP
- rs74510632
- Type
- single nucleotide variant
- Location
- chr19:46701084 (GRCh38)
- Gene constraint
- LOEUF 0.381 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 69.85 · 4 PDB
Similar variants
- PKD2 p.Arg306Ter Pathogenic ★★ same residue
- PKD2 p.Arg306Gly Uncertain significance ★★ ⚠ same residue
- PKD2 p.Arg306Gln Uncertain significance ★ ⚠ same residue
- PKD2 c.1094+1G>A Pathogenic ★★ same type
- PKD2 c.1094+1G>C Pathogenic ★★ same type
- PKD2 c.1319+1G>A Pathogenic/Likely pathogenic ★★ same type
- PKD2 c.1320-2A>C Pathogenic/Likely pathogenic ★★ same type
- PKD2 c.1548+1G>A Pathogenic/Likely 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/prkd2-p-cys306 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown