Is KCND3 p.Asp263= (c.789C>T) pathogenic?

KCND3 p.Asp263= (c.789C>T) is classified Benign/Likely benign in KCND3 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-09-27). Rare (popmax 0.107%, eas); Associated with Cardiovascular phenotype.

What condition is associated with KCND3 p.Asp263= (c.789C>T)?

KCND3 p.Asp263= (c.789C>T) is associated with Cardiovascular phenotype, spinocerebellar ataxia type 19/22 (ClinVar).

How common is KCND3 p.Asp263= (c.789C>T) in the general population?

KCND3 p.Asp263= (c.789C>T) is rare (popmax 0.107%, eas) (gnomAD).

KCND3 p.Asp263=

c.789C>T · rs373264592 · VCV695706

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

rare (popmax 0.107%, eas)

Conditions

Cardiovascular phenotype

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 -0.63	GERP -3.6
Overall
CADD	9.634	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.107% East Asian · 48/44,850 alleles

Filtering AF 0.0829% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0744%

Overall 0.00545% 88/1,614,118 alleles · rare exomes 59/1,461,888 · genomes 29/152,230 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.107%	934
African / African-American	0.036%	2,778
Admixed American	0.015%	6,668
Remaining individualsnot grpmax-eligible	0.0064%	15,628

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: KCND3
Protein: p.Asp263=
Coding: c.789C>T
MANE Select: NM_001378969
dbSNP: rs373264592
Type: single nucleotide variant
Location: chr1:111981938 (GRCh38)
Gene constraint: LOEUF 0.303 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 71.32 · 6 PDB
Residue 263: an α-helix

Full KCND3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: spinocerebellar ataxia type 19/22

Similar variants

KCND3 p.Arg290Gln Likely pathogenic ★★ same condition
KCND3 p.Gly384Ser Pathogenic/Likely pathogenic ★★ same condition
KCND3 p.Pro375Ser Pathogenic/Likely pathogenic ★★ same condition
KCND3 p.Thr377Met Pathogenic ★★ same condition
KCND3 p.Val392Ile Pathogenic/Likely pathogenic ★★ same condition
KCND3 p.Ala144Thr Uncertain significance ★★ ⚠ same condition
KCND3 p.Ala15Val Uncertain significance ★★ ⚠ same condition
KCND3 p.Ala172Thr Uncertain significance ★★ ⚠ 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/kcnd3-p-asp263 (accessed [today's date]).

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