Is EEF1B2 p.Ser128Ter (c.383C>A) pathogenic?

EEF1B2 p.Ser128Ter (c.383C>A) is classified Pathogenic in EEF1B2 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-08-05). Absent from gnomAD v4.1; Associated with intellectual disability.

What condition is associated with EEF1B2 p.Ser128Ter (c.383C>A)?

EEF1B2 p.Ser128Ter (c.383C>A) is associated with intellectual disability (ClinVar).

How common is EEF1B2 p.Ser128Ter (c.383C>A) in the general population?

EEF1B2 p.Ser128Ter (c.383C>A) is absent from gnomAD v4.1 (gnomAD).

EEF1B2 p.Ser128Ter

c.383C>A · rs1576016842 · VCV689450

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

intellectual disability

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function
NMD	predicted	premature termination codon in exon 4 of 6
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 1.3, phastCons 1
Overall
CADD	41.0	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: EEF1B2
Protein: p.Ser128Ter
Coding: c.383C>A
MANE Select: NM_001959
dbSNP: rs1576016842
Type: single nucleotide variant
Location: chr2:206162090 (GRCh38)
Gene constraint: LOEUF 0.688 · pLI 0.21 (gnomAD)
Structure: AlphaFold pLDDT 77.83 · 2 PDB

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

Disease context

intellectual disability — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

EEF1B2 c.80+1G>C 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
EEF1B2 p.Asp99Gly 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-ser128ter (accessed [today's date]).

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