Is PKD1 p.Val2002Phe (c.6004G>T) pathogenic?

PKD1 p.Val2002Phe (c.6004G>T) is classified Uncertain significance in PKD1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-11-22). AlphaMissense: likely pathogenic (0.8007); No allele count reported in gnomAD v4.1 (AN 1,600,782); Associated with Inborn genetic diseases.

What condition is associated with PKD1 p.Val2002Phe (c.6004G>T)?

PKD1 p.Val2002Phe (c.6004G>T) is associated with Inborn genetic diseases (ClinVar).

How common is PKD1 p.Val2002Phe (c.6004G>T) in the general population?

PKD1 p.Val2002Phe (c.6004G>T) is no allele count reported in gnomAD v4.1 (AN 1,600,782) (gnomAD).

What do computational predictors say about PKD1 p.Val2002Phe (c.6004G>T)?

AlphaMissense predicts likely pathogenic (score 0.8007) — an in-silico prediction, not a clinical call.

PKD1 p.Val2002Phe

c.6004G>T · rs1382000376 · VCV3213488

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8007 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,600,782)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.8007	likely pathogenic · top 10% in PKD1
REVEL	0.414	indeterminate
SaProt	—	not scored · why
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.9	GERP 2.2, phastCons 1
Regional constraint	o/e 1.08	unconstrained · MANE · 7,908 bp · p 6.5e-05 · regional, not allelic
Overall
CADD	24.8	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL is an independent agreement signal.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,600,782). 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.Val2002Phe
Coding: c.6004G>T
MANE Select: NM_001009944
dbSNP: rs1382000376
Type: single nucleotide variant
Location: chr16:2109163 (GRCh38)
Gene constraint: LOEUF 0.364 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 2002: the pkd 16 domain

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PKD1 p.Val2002Asp Conflicting classifications of pathogenicity ★ same residue
PKD1 p.Val2002Ile Uncertain significance ★ ⚠ same residue
PKD1 c.11017-10C>A Pathogenic/Likely pathogenic ★★ same condition
PKD1 c.1385+1G>C Pathogenic/Likely pathogenic ★★ same condition
PKD1 c.3295+1G>C Pathogenic/Likely pathogenic ★★ same condition
PKD1 p.Arg138Ter Pathogenic ★★ same condition
PKD1 p.Arg4021Ter Pathogenic ★★ same condition
PKD1 p.Gln1172Ter 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-val2002phe (accessed [today's date]).

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