Is PKD1 p.Pro299fs (c.896_897del) pathogenic?

PKD1 p.Pro299fs (c.896897del) is classified Pathogenic in PKD1 (ClinVar, Multiple submitters, 6 submitters; last evaluated 2025-05-01). No gnomAD frequency available for this variant; Associated with PKD1-Biallelic Autosomal Recessive Polycystic Kidney Disease.

How common is PKD1 p.Pro299fs (c.896_897del) in the general population?

PKD1 p.Pro299fs (c.896_897del) is no gnomAD frequency available for this variant (gnomAD).

PKD1 p.Pro299fs

Q: What condition is associated with PKD1 p.Pro299fs (c.896_897del)?

PKD1 p.Pro299fs (c.896_897del) is associated with PKD1-Biallelic Autosomal Recessive Polycystic Kidney Disease, polycystic kidney disease 1 (ClinVar).

c.896_897del · rs1555459084 · VCV522395

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

PKD1-Biallelic Autosomal Recessive Polycystic Kidney Disease

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 5 of 46
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -1.8	GERP -2.5
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.Pro299fs
Coding: c.896_897del
MANE Select: NM_001009944
dbSNP: rs1555459084
Type: Deletion
Location: chr16:2118095 (GRCh38)
Gene constraint: LOEUF 0.364 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 299: the pkd 1 domain

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

Disease context

PKD1-Biallelic Autosomal Recessive Polycystic Kidney Disease

Also linked: polycystic kidney disease 1

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-pro299fs (accessed [today's date]).

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