Is PKD1 p.Pro1069fs (c.3205_3235del) pathogenic?

PKD1 p.Pro1069fs (c.32053235del) is classified Pathogenic in PKD1 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-04-25). No gnomAD frequency available for this variant; Associated with polycystic kidney disease 1.

What condition is associated with PKD1 p.Pro1069fs (c.3205_3235del)?

PKD1 p.Pro1069fs (c.3205_3235del) is associated with polycystic kidney disease 1 (ClinVar).

How common is PKD1 p.Pro1069fs (c.3205_3235del) in the general population?

PKD1 p.Pro1069fs (c.3205_3235del) is no gnomAD frequency available for this variant (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.Pro1069fs

c.3205_3235del · rs2092538008 · VCV972674

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

polycystic kidney disease 1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 14 of 46
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.8	GERP 1.4, phastCons 1
Region caveats
Repeat context	seg dup	· reads may not map uniquely · confidence, not pathogenicity

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: PKD1
Protein: p.Pro1069fs
Coding: c.3205_3235del
MANE Select: NM_001009944
dbSNP: rs2092538008
Type: Deletion
Location: chr16:2112400 (GRCh38)
Gene constraint: LOEUF 0.364 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 1069: the pkd 5 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 c.10167+25_10167+43del Pathogenic/Likely pathogenic ★★ same condition
PKD1 c.12003+14_12003+33del Pathogenic/Likely pathogenic ★★ same condition
PKD1 c.3296-4_3304del Pathogenic/Likely pathogenic ★★ same condition
PKD1 c.8017-2_8017-1del Pathogenic ★★ same condition
PKD1 p.Ala1458fs Pathogenic ★★ same condition
PKD1 p.Ala3082fs Pathogenic ★★ same condition
PKD1 p.Ala4077fs Pathogenic/Likely pathogenic ★★ same condition
PKD1 p.Ala5fs 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-pro1069fs (accessed [today's date]).

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