Is EEF1B2 p.Pro30= (c.90A>G) pathogenic?

EEF1B2 p.Pro30= (c.90A>G) is classified Likely benign in EEF1B2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-08-01). Very rare (popmax 0.000424%, nfe).

How common is EEF1B2 p.Pro30= (c.90A>G) in the general population?

EEF1B2 p.Pro30= (c.90A>G) is very rare (popmax 0.000424%, nfe) (gnomAD).

EEF1B2 p.Pro30=

c.90A>G · rs755528110 · VCV2651837

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.000424%, nfe)

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 -4.7	GERP -4.5
Overall
CADD	5.905	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000424% European (non-Finnish) · 5/1,180,012 alleles

Filtering AF 0.000124% ClinGen BA1/BS1 input FAF95, joint · FAF99 9e-05%

Overall 0.000342% 5/1,461,872 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: EEF1B2
Protein: p.Pro30=
Coding: c.90A>G
MANE Select: NM_001959
dbSNP: rs755528110
Type: single nucleotide variant
Location: chr2:206160597 (GRCh38)
Gene constraint: LOEUF 0.688 · pLI 0.21 (gnomAD)
Structure: AlphaFold pLDDT 77.83 · 2 PDB
Residue 30: the gst c-terminal domain

Full EEF1B2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

EEF1B2 c.80+1G>C Pathogenic ★ same type
EEF1B2 p.Ser128Ter Pathogenic ★ same type
EEF1B2 p.Ala115Thr Uncertain significance ★ ⚠ same type
EEF1B2 p.Ala167Thr Uncertain significance ★ ⚠ same type
EEF1B2 p.Asp102Asn Uncertain significance ★ ⚠ same type
EEF1B2 p.Asp108Glu Uncertain significance ★ ⚠ same type
EEF1B2 p.Asp201Glu Uncertain significance ★ ⚠ same type
EEF1B2 p.Asp21Asn Uncertain significance ★ ⚠ 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/eef1b2-p-pro30 (accessed [today's date]).

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