Is EEF2 p.Gly620fs (c.1859del) pathogenic?

EEF2 p.Gly620fs (c.1859del) is classified Uncertain significance in EEF2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-03-13). Absent from gnomAD.

How common is EEF2 p.Gly620fs (c.1859del) in the general population?

EEF2 p.Gly620fs (c.1859del) is absent from gnomAD (gnomAD).

EEF2 p.Gly620fs

c.1859del · rs2512199758 · VCV2110815

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a LoF-intolerant gene
NMD	predicted	premature termination codon in exon 12 of 15
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -8.4	GERP -4.5

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: EEF2
Protein: p.Gly620fs
Coding: c.1859del
MANE Select: NM_001961
dbSNP: rs2512199758
Type: Deletion
Location: chr19:3978027 (GRCh38)
Gene constraint: LOEUF 0.39 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 89.97 · 26 PDB

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

Similar variants

EEF2 c.1150+1del Uncertain significance ★ same type
EEF2 c.1346+2_1346+3del Uncertain significance ★ same type
EEF2 p.Ala148fs Uncertain significance ★ same type
EEF2 p.Gly242fs Uncertain significance ★ same type
EEF2 p.Phe289del Uncertain significance ★ same type
EEF2 c.1606-13del 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-gly620fs (accessed [today's date]).

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