PKDCC p.Ser394=
c.1182C>T · rs55771746 · VCV1626252
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.62%, eas)
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 -11 | GERP -2.7 |
| Overall | ||
| CADD | 6.089 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.62%
East Asian · 725/44,874 alleles
Filtering AF
1.52%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.48%
Overall
0.0479%
773/1,613,696 alleles · low-frequency
exomes 681/1,461,424 · genomes 92/152,272 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.62% | 62 |
| Remaining individualsnot grpmax-eligible | 0.0384% | 2,604 |
| South Asian | 0.0033% | 30,331 |
| Admixed American | 0.00167% | 59,998 |
| European (non-Finnish) | 0.00161% | 62,104 |
| African / African-American | 0.00133% | 75,028 |
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.Ser394=
- Coding
- c.1182C>T
- MANE Select
- NM_138370
- dbSNP
- rs55771746
- Type
- single nucleotide variant
- Location
- chr2:42055353 (GRCh38)
- Gene constraint
- LOEUF 1.15 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.96
- Residue 394
- a UniProt-annotated variant site (in rlsdf); the protein kinase domain
Similar variants
- 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
- PKDCC p.Asp89His 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-ser394 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown