PKD1 p.Pro2201=
c.6603A>G · rs751666019 · VCV2646009
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0417%, afr)
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 -6.7 | GERP -4.2 |
| Overall | ||
| CADD | 0.209 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0417%
African / African-American · 31/74,368 alleles
Filtering AF
0.0302%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0262%
Overall
0.0141%
223/1,581,090 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0417% | 2,399 |
| Middle Eastern | 0.0226% | 4,418 |
| European (non-Finnish) | 0.0146% | 6,848 |
| Remaining individualsnot grpmax-eligible | 0.0131% | 7,628 |
| Admixed American | 0.0108% | 9,247 |
| South Asian | 0.00794% | 12,595 |
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.Pro2201=
- Coding
- c.6603A>G
- MANE Select
- NM_001009944
- dbSNP
- rs751666019
- Type
- single nucleotide variant
- Location
- chr16:2108564 (GRCh38)
- Gene constraint
- LOEUF 0.364 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Residue 2201
- the rej domain
Similar variants
- PKD1 p.Pro2201Leu Uncertain significance ★ ⚠ same residue
- PKD1 p.Pro2201Ser Uncertain significance ★ ⚠ same residue
- PKD1 p.Pro2201fs Pathogenic ★ same residue
- PKD1 c.10619-2A>G Pathogenic ★★ same type
- PKD1 c.10821+1G>A Pathogenic/Likely pathogenic ★★ same type
- PKD1 c.10821+2T>G Pathogenic/Likely pathogenic ★★ same type
- PKD1 c.11017-10C>A Pathogenic/Likely pathogenic ★★ same type
- PKD1 c.11017-25A>C Likely pathogenic ★★ 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/pkd1-p-pro2201 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown