Is KCNC1 p.Pro85= (c.255G>A) pathogenic?

KCNC1 p.Pro85= (c.255G>A) is classified Likely benign in KCNC1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-11-09). Very rare (popmax 0.00424%, nfe); Associated with progressive myoclonic epilepsy type 7.

What condition is associated with KCNC1 p.Pro85= (c.255G>A)?

KCNC1 p.Pro85= (c.255G>A) is associated with progressive myoclonic epilepsy type 7 (ClinVar).

How common is KCNC1 p.Pro85= (c.255G>A) in the general population?

KCNC1 p.Pro85= (c.255G>A) is very rare (popmax 0.00424%, nfe) (gnomAD).

How is Progressive myoclonic epilepsy type 7 inherited?

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

KCNC1 p.Pro85=

c.255G>A · rs368634420 · VCV1123233

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00424%, nfe)

Conditions

progressive myoclonic epilepsy type 7

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 -2.3	GERP -4.1
Overall
CADD	7.952	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00424% European (non-Finnish) · 50/1,179,908 alleles

Filtering AF 0.00326% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00294%

Overall 0.00322% 52/1,613,598 alleles · very rare exomes 45/1,461,364 · genomes 7/152,234 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00424%	23,598
Remaining individualsnot grpmax-eligible	0.0016%	62,456
African / African-American	0.00133%	74,922

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: KCNC1
Protein: p.Pro85=
Coding: c.255G>A
MANE Select: NM_001112741
dbSNP: rs368634420
Type: single nucleotide variant
Location: chr11:17736257 (GRCh38)
Gene constraint: LOEUF 0.363 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 79.51 · 10 PDB
Residue 85: an α-helix

Full KCNC1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

progressive myoclonic epilepsy type 7 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Progressive myoclonic epilepsy type 7 (Orphanet):

Inheritance: Autosomal dominant
Onset: Childhood

Similar variants

KCNC1 p.Ala421Val Pathogenic/Likely pathogenic ★★ same condition
KCNC1 p.Arg320His Pathogenic/Likely pathogenic ★★ same condition
KCNC1 p.Thr399Met Pathogenic/Likely pathogenic ★★ same condition
KCNC1 p.Val425Met Pathogenic/Likely pathogenic ★★ same condition
KCNC1 p.Ala360Thr Uncertain significance ★★ ⚠ same condition
KCNC1 p.Ala418Ser Uncertain significance ★★ ⚠ same condition
KCNC1 p.Ala510Val Uncertain significance ★★ same condition
KCNC1 p.Ala555Val 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/kcnc1-p-pro85 (accessed [today's date]).

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