Is CERS1 p.Leu300= (c.898C>T) pathogenic?

CERS1 p.Leu300= (c.898C>T) is classified Likely benign in CERS1 (ClinVar, Multiple submitters, 6 submitters; last evaluated 2026-01-12). Rare (popmax 0.396%, mid); Associated with progressive myoclonic epilepsy type 8.

What condition is associated with CERS1 p.Leu300= (c.898C>T)?

CERS1 p.Leu300= (c.898C>T) is associated with progressive myoclonic epilepsy type 8 (ClinVar).

How common is CERS1 p.Leu300= (c.898C>T) in the general population?

CERS1 p.Leu300= (c.898C>T) is rare (popmax 0.396%, mid) (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.Leu300=

c.898C>T · rs373928623 · VCV475378

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

gnomAD v4.1

Rare

rare (popmax 0.396%, mid)

Conditions

progressive myoclonic epilepsy type 8

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 7.2	GERP 0.7, phastCons 1
Overall
CADD	16.61	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.396% Middle Eastern · 24/6,058 alleles

Filtering AF 0.273% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.233%

Overall 0.0484% 781/1,613,654 alleles · rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.396%	252
Ashkenazi Jewishnot grpmax-eligible	0.142%	704
Remaining individualsnot grpmax-eligible	0.064%	1,562
European (non-Finnish)	0.0505%	1,980
Admixed American	0.0467%	2,142
South Asian	0.0363%	2,758
Finnishnot grpmax-eligible	0.0172%	5,813
African / African-American	0.008%	12,504
East Asian	0.00223%	44,874

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.Leu300=
Coding: c.898C>T
MANE Select: NM_021267
dbSNP: rs373928623
Type: single nucleotide variant
Location: chr19:18879243 (GRCh38)
Gene constraint: LOEUF 0.685 · pLI 0.17 (gnomAD)
Structure: AlphaFold pLDDT 88.95
Residue 300: a UniProt-annotated variant site (in epm8); the tlc domain

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

Similar variants

CERS1 p.Ala117Ser Uncertain significance ★★ ⚠ same condition
CERS1 p.Ala165Thr Uncertain significance ★★ ⚠ same condition
CERS1 p.Ala266Val Uncertain significance ★★ ⚠ same condition
CERS1 p.Ala286Val Uncertain significance ★★ ⚠ same condition
CERS1 p.Ala304Val Uncertain significance ★★ ⚠ same condition
CERS1 p.Ala45Pro Uncertain significance ★★ ⚠ same condition
CERS1 p.Ala86Val Uncertain significance ★★ ⚠ same condition
CERS1 p.Ala97Thr 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/cers1-p-leu300 (accessed [today's date]).

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