Is PKD1 p.Pro1256= (c.3768G>A) pathogenic?

PKD1 p.Pro1256= (c.3768G>A) is classified Uncertain significance in PKD1 (ClinVar, Single submitter, 2 submitters; last evaluated 2024-01-24). Very rare (popmax 0.005%, amr); Associated with polycystic kidney disease 1.

What condition is associated with PKD1 p.Pro1256= (c.3768G>A)?

PKD1 p.Pro1256= (c.3768G>A) is associated with polycystic kidney disease 1 (ClinVar).

How common is PKD1 p.Pro1256= (c.3768G>A) in the general population?

PKD1 p.Pro1256= (c.3768G>A) is very rare (popmax 0.005%, amr) (gnomAD).

How is Autosomal dominant polycystic kidney disease inherited?

Typically Autosomal dominant (Orphanet). A genetic counselor can assess individual risk for a family.

PKD1 p.Pro1256=

c.3768G>A · rs770836714 · VCV3058317

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.005%, amr)

Conditions

polycystic kidney disease 1

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 -13	GERP -3.4
Overall
CADD	0.028	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.005% Admixed American · 3/59,950 alleles

Filtering AF 0.00133% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000668%

Overall 0.00118% 19/1,611,524 alleles · very rare exomes 15/1,459,328 · genomes 4/152,196 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.005%	19,983
East Asian	0.00223%	44,878
Remaining individualsnot grpmax-eligible	0.0016%	62,404
African / African-American	0.00134%	74,900
European (non-Finnish)	0.0011%	90,737

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.Pro1256=
Coding: c.3768G>A
MANE Select: NM_001009944
dbSNP: rs770836714
Type: single nucleotide variant
Location: chr16:2111399 (GRCh38)
Gene constraint: LOEUF 0.364 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 1256: the pkd 7 domain

Full PKD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

polycystic kidney disease 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Autosomal dominant polycystic kidney disease (Orphanet):

Inheritance: Autosomal dominant
Onset: Adolescent, Adult, Childhood
Prevalence: 1-5 / 10 000 (Europe)

Similar variants

PKD1 p.Pro1256Leu Uncertain significance ★★ ⚠ same residue
PKD1 c.10619-2A>G Pathogenic ★★ same condition
PKD1 c.10821+1G>A Pathogenic/Likely pathogenic ★★ same condition
PKD1 c.10821+2T>G Pathogenic/Likely pathogenic ★★ same condition
PKD1 c.11017-10C>A Pathogenic/Likely pathogenic ★★ same condition
PKD1 c.11017-25A>C Likely pathogenic ★★ same condition
PKD1 c.11017-25A>G Likely pathogenic ★★ same condition
PKD1 c.11269+1G>C 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-pro1256 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown