PRKD1 p.Pro35=
c.105C>T · rs200093824 · VCV731013
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.263%, nfe)
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 2.9 | GERP -1.1, phastCons 1 |
| Overall | ||
| CADD | 13.12 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.263%
European (non-Finnish) · 2,966/1,128,452 alleles
Filtering AF
0.255%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.252%
Overall
0.207%
3,114/1,503,708 alleles · rare
exomes 2,941/1,354,196 · genomes 173/149,512 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.263% | 380 |
| Remaining individualsnot grpmax-eligible | 0.112% | 890 |
| African / African-American | 0.0433% | 2,311 |
| Admixed American | 0.0389% | 2,570 |
| South Asian | 0.0273% | 3,664 |
| Finnishnot grpmax-eligible | 0.0209% | 4,788 |
| East Asian | 0.00564% | 17,720 |
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
- PRKD1
- Protein
- p.Pro35=
- Coding
- c.105C>T
- MANE Select
- NM_002742
- dbSNP
- rs200093824
- Type
- single nucleotide variant
- Location
- chr14:29927408 (GRCh38)
- Gene constraint
- LOEUF 0.762 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 68.99
Similar variants
- PRKD1 p.Pro35Ser Uncertain significance ★ ⚠ same residue
- PRKD1 p.Ala529Thr Uncertain significance ★★ ⚠ same type
- PRKD1 p.Arg201Trp Uncertain significance ★★ same type
- PRKD1 p.Arg203Lys Uncertain significance ★★ ⚠ same type
- PRKD1 p.Arg740Gln Uncertain significance ★★ ⚠ same type
- PRKD1 p.Asn498Ser Uncertain significance ★★ ⚠ same type
- PRKD1 p.Gln115His Uncertain significance ★★ ⚠ same type
- PRKD1 p.Gly486Arg 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/prkd1-p-pro35 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown