PKDCC p.Cys331=
c.993C>T · rs1389687516 · VCV2065028
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00134%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.57 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.9 | GERP -2.9 |
| Overall | ||
| CADD | 7.337 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00134%
African / African-American · 1/74,872 alleles
Filtering AF
0.000184%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000121%
Overall
0.000436%
7/1,606,124 alleles · very rare
exomes 7/1,453,812 · genomes 0/152,312 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00134% | 74,872 |
| European (non-Finnish) | 0.00051% | 196,007 |
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
- PKDCC
- Protein
- p.Cys331=
- Coding
- c.993C>T
- MANE Select
- NM_138370
- dbSNP
- rs1389687516
- Type
- single nucleotide variant
- Location
- chr2:42054266 (GRCh38)
- Gene constraint
- LOEUF 1.15 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.96
- Residue 331
- a UniProt-annotated variant site (in rlsdf); the protein kinase domain
Similar variants
- PKDCC p.Cys331Arg Uncertain significance ★★ ⚠ same residue
- PKDCC p.Leu262Arg Pathogenic/Likely pathogenic ★★ same type
- PKDCC c.640-12G>A Uncertain significance ★★ same type
- PKDCC p.Ala299Thr Uncertain significance ★★ ⚠ same type
- PKDCC p.Arg280Cys Uncertain significance ★★ ⚠ same type
- PKDCC p.Arg338Gln Uncertain significance ★★ ⚠ same type
- PKDCC p.Arg393Gln Uncertain significance ★★ ⚠ same type
- PKDCC p.Asp295Glu 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/pkdcc-p-cys331 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown