Is SGCE p.Leu413= (c.1237T>C) pathogenic?

SGCE p.Leu413= (c.1237T>C) is classified Likely benign in SGCE (ClinVar, Single submitter, 1 submitter; last evaluated 2026-01-12). Very rare (popmax 0.004%, afr); Associated with myoclonic dystonia 11.

What condition is associated with SGCE p.Leu413= (c.1237T>C)?

SGCE p.Leu413= (c.1237T>C) is associated with myoclonic dystonia 11 (ClinVar).

How common is SGCE p.Leu413= (c.1237T>C) in the general population?

SGCE p.Leu413= (c.1237T>C) is very rare (popmax 0.004%, afr) (gnomAD).

How is Myoclonus-dystonia syndrome inherited?

Typically Autosomal dominant, Not applicable (Orphanet). A genetic counselor can assess individual risk for a family.

SGCE p.Leu413=

c.1237T>C · rs147387740 · VCV1567807

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.004%, afr)

Conditions

myoclonic dystonia 11

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -1.3	GERP -3.1
Overall
CADD	4.62	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.004% African / African-American · 3/75,002 alleles

Filtering AF 0.00106% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000495%

Overall 0.000248% 4/1,612,014 alleles · very rare exomes 2/1,459,712 · genomes 2/152,302 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.004%	25,001
Admixed American	0.00167%	60,004

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: SGCE
Protein: p.Leu413=
Coding: c.1237T>C
MANE Select: NM_003919
dbSNP: rs147387740
Type: single nucleotide variant
Location: chr7:94598791 (GRCh38)

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

Disease context

myoclonic dystonia 11 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Myoclonus-dystonia syndrome (Orphanet):

Inheritance: Autosomal dominant, Not applicable
Onset: Adolescent, Adult, Childhood
Prevalence: 1-9 / 1 000 000 (Europe)

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/sgce-p-leu413 (accessed [today's date]).

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