Is PKD2 p.Asp780= (c.2340C>T) pathogenic?

PKD2 p.Asp780= (c.2340C>T) is classified Benign in PKD2 (ClinVar, Single submitter, 2 submitters; last evaluated 2025-07-16). Ultra-rare (popmax 0.0294%, afr); Associated with autosomal dominant polycystic kidney disease.

What condition is associated with PKD2 p.Asp780= (c.2340C>T)?

PKD2 p.Asp780= (c.2340C>T) is associated with autosomal dominant polycystic kidney disease (ClinVar).

How common is PKD2 p.Asp780= (c.2340C>T) in the general population?

PKD2 p.Asp780= (c.2340C>T) is ultra-rare (popmax 0.0294%, afr) (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.Asp780=

c.2340C>T · rs372745575 · VCV2874337

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0294%, afr)

Conditions

autosomal dominant polycystic kidney disease

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 -13	GERP -3.8
Overall
CADD	2.918	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0294% African / African-American · 22/74,738 alleles

Filtering AF 0.0199% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0168%

Overall 0.00218% 35/1,607,672 alleles · ultra-rare exomes 21/1,455,600 · genomes 14/152,072 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0294%	3,397
South Asian	0.0044%	22,743
Remaining individualsnot grpmax-eligible	0.00161%	62,258
European (non-Finnish)	0.000681%	146,789

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.Asp780=
Coding: c.2340C>T
MANE Select: NM_000297
dbSNP: rs372745575
Type: single nucleotide variant
Location: chr4:88065861 (GRCh38)
Structure: AlphaFold pLDDT 69.85 · 4 PDB
Residue 780: the protein kinase domain

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

Disease context

autosomal dominant polycystic kidney disease — 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

PKD2 p.Asp780Asn Uncertain significance ★★ ⚠ same residue
PKD2 p.Asp780His Uncertain significance ★★ same residue
PKD2 p.Asp780Glu Uncertain significance ★ ⚠ same residue
PKD2 c.1094+1G>A Pathogenic ★★ same condition
PKD2 c.1319+1G>A Pathogenic/Likely pathogenic ★★ same condition
PKD2 c.1548+1G>A Pathogenic/Likely pathogenic ★★ same condition
PKD2 c.1898+5G>A Pathogenic/Likely pathogenic ★★ same condition
PKD2 c.2019+1G>A 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-asp780 (accessed [today's date]).

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