Is KCNC1 p.Ser412= (c.1236C>T) pathogenic?

KCNC1 p.Ser412= (c.1236C>T) is classified Benign/Likely benign in KCNC1 (ClinVar, Multiple submitters, 8 submitters; last evaluated 2026-01-21). Rare (popmax 0.949%, afr); Associated with progressive myoclonic epilepsy type 7.

What condition is associated with KCNC1 p.Ser412= (c.1236C>T)?

KCNC1 p.Ser412= (c.1236C>T) is associated with progressive myoclonic epilepsy type 7 (ClinVar).

How common is KCNC1 p.Ser412= (c.1236C>T) in the general population?

KCNC1 p.Ser412= (c.1236C>T) is rare (popmax 0.949%, afr) (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.Ser412=

c.1236C>T · rs73424033 · VCV475347

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 8 submitters

gnomAD v4.1

Rare

rare (popmax 0.949%, afr)

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 -1.9	GERP -4.1
Overall
CADD	12.72	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.949% African / African-American · 712/75,038 alleles

Filtering AF 0.891% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.868%

Overall 0.0551% 890/1,614,176 alleles · rare exomes 480/1,461,868 · genomes 410/152,308 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.949%	105
Middle Eastern	0.0825%	1,212
Remaining individualsnot grpmax-eligible	0.0688%	1,454
Admixed American	0.0616%	1,622
South Asian	0.00769%	13,012
European (non-Finnish)	0.0072%	13,883
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,606

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.Ser412=
Coding: c.1236C>T
MANE Select: NM_001112741
dbSNP: rs73424033
Type: single nucleotide variant
Location: chr11:17772330 (GRCh38)
Gene constraint: LOEUF 0.363 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 79.51 · 10 PDB
Residue 412: 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-ser412 (accessed [today's date]).

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