Is EPM2A p.Ala14= (c.42C>G) pathogenic?

EPM2A p.Ala14= (c.42C>G) is classified Likely benign in EPM2A (ClinVar, Single submitter, 1 submitter; last evaluated 2024-08-13). Very rare (popmax 0.00158%, afr); Associated with progressive myoclonus epilepsy.

What condition is associated with EPM2A p.Ala14= (c.42C>G)?

EPM2A p.Ala14= (c.42C>G) is associated with progressive myoclonus epilepsy (ClinVar).

How common is EPM2A p.Ala14= (c.42C>G) in the general population?

EPM2A p.Ala14= (c.42C>G) is very rare (popmax 0.00158%, afr) (gnomAD).

EPM2A p.Ala14=

c.42C>G · rs2128650003 · VCV1637584

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00158%, afr)

Conditions

progressive myoclonus epilepsy

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 1.2	GERP -0.24, phastCons 1
Overall
CADD	9.824	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00158% African / African-American · 1/63,354 alleles

Filtering AF 3.4e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.3e-05%

Overall 0.000244% 3/1,231,824 alleles · very rare exomes 3/1,080,542 · genomes 0/151,282 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00158%	63,354
European (non-Finnish)	0.000203%	491,894

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: EPM2A
Protein: p.Ala14=
Coding: c.42C>G
MANE Select: NM_005670
dbSNP: rs2128650003
Type: single nucleotide variant
Location: chr6:145735457 (GRCh38)
Gene constraint: LOEUF 1.191 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 34.25 · 2 PDB
Residue 14: the 'disordered' region; the cbm20 domain; an α-helix

Full EPM2A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

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

Similar variants

EPM2A c.301+1G>T Pathogenic ★★ same condition
EPM2A c.302-1G>C Pathogenic/Likely pathogenic ★★ same condition
EPM2A c.302-2A>G Pathogenic ★★ same condition
EPM2A p.Arg108Cys Pathogenic/Likely pathogenic ★★ same condition
EPM2A p.Arg171His Pathogenic/Likely pathogenic ★★ same condition
EPM2A p.Arg241Ter Pathogenic/Likely pathogenic ★★ same condition
EPM2A p.Gly279Cys Pathogenic/Likely pathogenic ★★ same condition
EPM2A p.Gly279Ser Pathogenic/Likely pathogenic ★★ 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/epm2a-p-ala14 (accessed [today's date]).

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