Is EEF1A2 p.His15= (c.45C>T) pathogenic?

EEF1A2 p.His15= (c.45C>T) is classified Likely benign in EEF1A2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-25). Ultra-rare (popmax 0.0134%, eas); Associated with developmental and epileptic encephalopathy, 33.

What condition is associated with EEF1A2 p.His15= (c.45C>T)?

EEF1A2 p.His15= (c.45C>T) is associated with developmental and epileptic encephalopathy, 33 (ClinVar).

How common is EEF1A2 p.His15= (c.45C>T) in the general population?

EEF1A2 p.His15= (c.45C>T) is ultra-rare (popmax 0.0134%, eas) (gnomAD).

EEF1A2 p.His15=

Q: How is Non-specific early-onset epileptic encephalopathy inherited?

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

c.45C>T · rs546748631 · VCV1147206

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0134%, eas)

Conditions

developmental and epileptic encephalopathy, 33

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>C here scores Δ0.31 · evaluated, not missing
Constraint at this position
Conservation	phyloP -2.8	GERP -3.8
Overall
CADD	6.797	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0134% East Asian · 6/44,876 alleles

Filtering AF 0.00579% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00394%

Overall 0.000806% 13/1,612,960 alleles · ultra-rare exomes 10/1,460,634 · genomes 3/152,326 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0134%	7,479
African / African-American	0.00533%	18,763
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,588
Remaining individualsnot grpmax-eligible	0.0016%	62,482
European (non-Finnish)	8.48e-05%	1,179,869

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: EEF1A2
Protein: p.His15=
Coding: c.45C>T
MANE Select: NM_001958
dbSNP: rs546748631
Type: single nucleotide variant
Location: chr20:63497719 (GRCh38)
Gene constraint: LOEUF 0.314 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 88.70 · 2 PDB
Residue 15: the tr-type g domain; the 'g1' region

Full EEF1A2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

developmental and epileptic encephalopathy, 33 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Non-specific early-onset epileptic encephalopathy (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, Not applicable
Onset: Infancy, Neonatal

Similar variants

EEF1A2 p.His15Asn Likely pathogenic ★ same residue
EEF1A2 p.His15Tyr Uncertain significance ★ ⚠ same residue
EEF1A2 p.Arg266Trp Pathogenic/Likely pathogenic ★★ same condition
EEF1A2 p.Arg423Cys Pathogenic/Likely pathogenic ★★ same condition
EEF1A2 p.Arg69Cys Pathogenic ★★ same condition
EEF1A2 p.Asp91Asn Pathogenic ★★ ⚠ same condition
EEF1A2 p.Asp97Asn Pathogenic/Likely pathogenic ★★ same condition
EEF1A2 p.Glu122Lys 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/eef1a2-p-his15 (accessed [today's date]).

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