PKD1 p.Ser366=
c.1098G>C · rs1450062463 · VCV3036499
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000853%, nfe)
Conditions
1
PKD1-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.24 | acceptor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -10 | GERP -2.8 |
| Overall | ||
| CADD | 1.051 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000853%
European (non-Finnish) · 7/820,802 alleles
Filtering AF
0.000355%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000228%
Overall
0.000595%
7/1,177,086 alleles · very rare
exomes 7/1,024,892 · genomes 0/152,194 · 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
- PKD1
- Protein
- p.Ser366=
- Coding
- c.1098G>C
- MANE Select
- NM_001009944
- dbSNP
- rs1450062463
- Type
- single nucleotide variant
- Location
- chr16:2117894 (GRCh38)
- Gene constraint
- LOEUF 0.364 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Disease context
PKD1-related disorder
Similar variants
- PKD1 p.Ser366Ter Likely pathogenic ★ same residue
- PKD1 p.Ser366Leu Uncertain significance ★ ⚠ same residue
- PKD1 p.Ser366Pro Uncertain significance ★ ⚠ same residue
- PKD1 p.Ser366Trp Conflicting classifications of pathogenicity ★ ⚠ same residue
- PKD1 c.11269+1G>C Pathogenic ★★ same condition
- PKD1 c.11412-1G>A Pathogenic/Likely pathogenic ★★ same condition
- PKD1 c.11713-2A>G Pathogenic ★★ same condition
- PKD1 c.215+5G>A Likely pathogenic ★★ same condition
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/pkd1-p-ser366 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown