Is CERS1 p.Ala96= (c.288C>T) pathogenic?

CERS1 p.Ala96= (c.288C>T) is classified Likely benign in CERS1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-02-02). Very rare (popmax 0.00447%, eas); Associated with progressive myoclonic epilepsy type 8.

What condition is associated with CERS1 p.Ala96= (c.288C>T)?

CERS1 p.Ala96= (c.288C>T) is associated with progressive myoclonic epilepsy type 8 (ClinVar).

How common is CERS1 p.Ala96= (c.288C>T) in the general population?

CERS1 p.Ala96= (c.288C>T) is very rare (popmax 0.00447%, eas) (gnomAD).

How is Progressive myoclonic epilepsy type 8 inherited?

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

CERS1 p.Ala96=

c.288C>T · rs2056549006 · VCV2808042

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00447%, eas)

Conditions

progressive myoclonic epilepsy type 8

⚠ 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 -7.3	GERP -3.2
Overall
CADD	2.736	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00447% East Asian · 2/44,788 alleles

Filtering AF 0.00074% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000277%

Overall 0.000435% 7/1,610,422 alleles · very rare exomes 6/1,458,272 · genomes 1/152,150 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00447%	22,394
African / African-American	0.00267%	37,439
European (non-Finnish)	0.000255%	392,927

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: CERS1
Protein: p.Ala96=
Coding: c.288C>T
MANE Select: NM_021267
dbSNP: rs2056549006
Type: single nucleotide variant
Location: chr19:18893537 (GRCh38)

Full CERS1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

progressive myoclonic epilepsy type 8 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Progressive myoclonic epilepsy type 8 (Orphanet):

Inheritance: Autosomal recessive
Onset: Adolescent, Childhood

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/cers1-p-ala96 (accessed [today's date]).

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