Is KCND2 p.Val267= (c.801G>A) pathogenic?

KCND2 p.Val267= (c.801G>A) is classified Benign in KCND2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-11). Ultra-rare (popmax 0.0854%, afr); Associated with Early Myoclonic Encephalopathy.

What condition is associated with KCND2 p.Val267= (c.801G>A)?

KCND2 p.Val267= (c.801G>A) is associated with Early Myoclonic Encephalopathy (ClinVar).

How common is KCND2 p.Val267= (c.801G>A) in the general population?

KCND2 p.Val267= (c.801G>A) is ultra-rare (popmax 0.0854%, afr) (gnomAD).

KCND2 p.Val267=

c.801G>A · rs375854186 · VCV460206

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0854%, afr)

Conditions

Early Myoclonic Encephalopathy

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 5.2	GERP 0.98, phastCons 1
Overall
CADD	8.751	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0854% African / African-American · 64/74,908 alleles

Filtering AF 0.0686% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0625%

Overall 0.0049% 79/1,613,786 alleles · ultra-rare exomes 53/1,461,890 · genomes 26/151,896 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0854%	1,170
Middle Eastern	0.033%	3,031
Remaining individualsnot grpmax-eligible	0.0112%	8,929
Admixed American	0.00167%	59,992
European (non-Finnish)	0.000424%	235,990

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: KCND2
Protein: p.Val267=
Coding: c.801G>A
MANE Select: NM_012281
dbSNP: rs375854186
Type: single nucleotide variant
Location: chr7:120275433 (GRCh38)
Gene constraint: LOEUF 0.428 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 72.28 · 16 PDB
Residue 267: an α-helix

Full KCND2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Early Myoclonic Encephalopathy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

KCND2 p.Pro403Ala Pathogenic/Likely pathogenic ★★ same condition
KCND2 c.1374+3A>G Uncertain significance ★★ same condition
KCND2 c.1468-3C>T Uncertain significance ★★ same condition
KCND2 p.Ala321Val Uncertain significance ★★ ⚠ same condition
KCND2 p.Ala399Ser Uncertain significance ★★ ⚠ same condition
KCND2 p.Arg147His Uncertain significance ★★ ⚠ same condition
KCND2 p.Arg533Ter Uncertain significance ★★ same condition
KCND2 p.Asp153Val 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/kcnd2-p-val267 (accessed [today's date]).

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