Is SGCE p.Asn170= (c.510T>C) pathogenic?

SGCE p.Asn170= (c.510T>C) is classified Conflicting classifications of pathogenicity in SGCE (ClinVar, Conflicting submitters, 4 submitters; last evaluated 2025-05-19). Ultra-rare (popmax 0.085%, amr); Associated with myoclonic dystonia 11.

What condition is associated with SGCE p.Asn170= (c.510T>C)?

SGCE p.Asn170= (c.510T>C) is associated with myoclonic dystonia 11 (ClinVar).

How common is SGCE p.Asn170= (c.510T>C) in the general population?

SGCE p.Asn170= (c.510T>C) is ultra-rare (popmax 0.085%, amr) (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.Asn170=

c.510T>C · rs55853245 · VCV360994

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.085%, amr)

Conditions

myoclonic dystonia 11

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 -2.5	GERP -2.2
Overall
CADD	5.496	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.085% Admixed American · 51/60,016 alleles

Filtering AF 0.0663% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0598%

Overall 0.019% 306/1,614,018 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.085%	1,177
European (non-Finnish)	0.0207%	4,836
Remaining individualsnot grpmax-eligible	0.0128%	7,813
African / African-American	0.00267%	37,518
Finnishnot grpmax-eligible	0.00156%	64,022

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.Asn170=
Coding: c.510T>C
MANE Select: NM_022900 · reported on NM_003919
dbSNP: rs55853245
Type: single nucleotide variant
Location: chr7:94618910 (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-asn170 (accessed [today's date]).

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