Is PKD2 p.Ser820= (c.2460C>T) pathogenic?

PKD2 p.Ser820= (c.2460C>T) is classified Benign/Likely benign in PKD2 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2025-11-27). Rare (popmax 0.706%, sas); Associated with polycystic kidney disease 2.

What condition is associated with PKD2 p.Ser820= (c.2460C>T)?

PKD2 p.Ser820= (c.2460C>T) is associated with polycystic kidney disease 2, autosomal dominant polycystic kidney disease (ClinVar).

How common is PKD2 p.Ser820= (c.2460C>T) in the general population?

PKD2 p.Ser820= (c.2460C>T) is rare (popmax 0.706%, sas) (gnomAD).

How is Autosomal dominant polycystic kidney disease inherited?

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

PKD2 p.Ser820=

c.2460C>T · rs572822238 · VCV1336016

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Rare

rare (popmax 0.706%, sas)

Conditions

polycystic kidney disease 2

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 -3.9	GERP -2
Overall
CADD	4.743	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.706% South Asian · 643/91,072 alleles

Filtering AF 0.661% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.643%

Overall 0.0429% 693/1,613,746 alleles · rare exomes 656/1,461,520 · genomes 37/152,226 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.706%	142
Remaining individualsnot grpmax-eligible	0.0368%	2,717
Middle Eastern	0.033%	3,031
African / African-American	0.004%	24,999
European (non-Finnish)	0.00178%	56,176
Admixed American	0.00167%	60,008

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: PKD2
Protein: p.Ser820=
Coding: c.2460C>T
MANE Select: NM_000297
dbSNP: rs572822238
Type: single nucleotide variant
Location: chr4:88067999 (GRCh38)
Structure: AlphaFold pLDDT 69.85 · 4 PDB

Full PKD2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

polycystic kidney disease 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: autosomal dominant polycystic kidney disease

For Autosomal dominant polycystic kidney disease (Orphanet):

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

Similar variants

PKD2 c.1094+1G>A Pathogenic ★★ same condition
PKD2 c.1094+1G>C Pathogenic ★★ same condition
PKD2 c.1319+1G>A Pathogenic/Likely pathogenic ★★ same condition
PKD2 c.1320-2A>C Pathogenic/Likely pathogenic ★★ same condition
PKD2 c.1548+1G>A Pathogenic/Likely pathogenic ★★ same condition
PKD2 c.1549-1G>A Pathogenic/Likely pathogenic ★★ same condition
PKD2 c.1716+2T>A Pathogenic/Likely pathogenic ★★ same condition
PKD2 c.1898+5G>A Pathogenic/Likely 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/pkd2-p-ser820 (accessed [today's date]).

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