Is EEF2 p.Ser113del (c.333CTC[1]) pathogenic?

EEF2 p.Ser113del (c.333CTC[1]) is classified Uncertain significance in EEF2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-03-03). Very rare (popmax 0.000169%, nfe); Associated with neurodevelopmental disorder.

What condition is associated with EEF2 p.Ser113del (c.333CTC[1])?

EEF2 p.Ser113del (c.333CTC[1]) is associated with neurodevelopmental disorder (ClinVar).

How common is EEF2 p.Ser113del (c.333CTC[1]) in the general population?

EEF2 p.Ser113del (c.333CTC[1]) is very rare (popmax 0.000169%, nfe) (gnomAD).

EEF2 p.Ser113del

c.333CTC[1] · rs2512206892 · VCV2789622

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.000169%, nfe)

Conditions

neurodevelopmental disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -15	GERP -4.5

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000169% European (non-Finnish) · 2/1,180,004 alleles

Filtering AF 2.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.1e-05%

Overall 0.000137% 2/1,461,868 alleles · very rare

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: EEF2
Protein: p.Ser113del
Coding: c.333CTC[1]
MANE Select: NM_001961
dbSNP: rs2512206892
Type: Microsatellite
Location: chr19:3983172 (GRCh38)
Gene constraint: LOEUF 0.39 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 89.97 · 26 PDB
Residue 113: the tr-type g domain; an α-helix

Full EEF2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

neurodevelopmental disorder — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

EEF2 p.Ser113= Likely benign ★ same residue
EEF2 c.219-9_219-6del Uncertain significance ★ same type
EEF2 p.Lys439del Uncertain significance ★ same type
EEF2 p.Val813_Phe814insTer Uncertain significance ★ same type
EEF2 c.898-20_898-14del Likely benign ★ same type

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/eef2-p-ser113del (accessed [today's date]).

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