Is PKD1 p.Ser1663del (c.4988_4990del) pathogenic?

PKD1 p.Ser1663del (c.49884990del) is classified Conflicting classifications of pathogenicity in PKD1 (ClinVar, Conflicting submitters, 3 submitters; last evaluated 2022-08-03). No gnomAD frequency available for this variant; Associated with polycystic kidney disease 1.

What condition is associated with PKD1 p.Ser1663del (c.4988_4990del)?

PKD1 p.Ser1663del (c.4988_4990del) is associated with polycystic kidney disease 1 (ClinVar).

How common is PKD1 p.Ser1663del (c.4988_4990del) in the general population?

PKD1 p.Ser1663del (c.4988_4990del) 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.Ser1663del

c.4988_4990del · rs1596556896 · VCV636752

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 3 submitters

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.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 3.3	GERP 0.12, phastCons 1
Region caveats
Repeat context	seg dup	· reads may not map uniquely · confidence, not pathogenicity

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.Ser1663del
Coding: c.4988_4990del
MANE Select: NM_001009944
dbSNP: rs1596556896
Type: Deletion
Location: chr16:2110177 (GRCh38)
Gene constraint: LOEUF 0.364 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 1663: the pkd 12 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-ser1663del (accessed [today's date]).

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