PKD1 p.Ser3002=
c.9006G>A · rs367709319 · VCV3058400
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.225%, sas)
Conditions
1
Inborn genetic diseases
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 Δ0.54 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -13 | GERP -4.4 |
| Overall | ||
| CADD | 0.126 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.225%
South Asian · 205/91,000 alleles
Filtering AF
0.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.19%
Overall
0.0138%
223/1,611,118 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.225% | 444 |
| Middle Eastern | 0.0409% | 2,443 |
| Remaining individualsnot grpmax-eligible | 0.00321% | 31,168 |
| African / African-American | 0.00267% | 37,502 |
| East Asian | 0.00223% | 44,880 |
| Admixed American | 0.00167% | 60,016 |
| European (non-Finnish) | 0.000848% | 117,975 |
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.Ser3002=
- Coding
- c.9006G>A
- MANE Select
- NM_001009944
- dbSNP
- rs367709319
- Type
- single nucleotide variant
- Location
- chr16:2102576 (GRCh38)
- Gene constraint
- LOEUF 0.364 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Residue 3002
- the gain-b domain
Similar variants
- PKD1 p.Ser3002Ter Pathogenic ★ same residue
- PKD1 p.Ser3002Leu Uncertain significance ★ same residue
- PKD1 c.11017-10C>A Pathogenic/Likely pathogenic ★★ same condition
- PKD1 c.1385+1G>C Pathogenic/Likely pathogenic ★★ same condition
- PKD1 c.3295+1G>C Pathogenic/Likely pathogenic ★★ same condition
- PKD1 p.Arg138Ter Pathogenic ★★ same condition
- PKD1 p.Arg4021Ter Pathogenic ★★ same condition
- PKD1 p.Gln1172Ter 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-ser3002 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown