Is EFTUD2 p.Ser866fs (c.2595dup) pathogenic?

EFTUD2 p.Ser866fs (c.2595dup) is classified Pathogenic in EFTUD2 (ClinVar, Single submitter, 1 submitter; last evaluated 2016-04-04). No gnomAD frequency available for this variant; Associated with Inborn genetic diseases.

What condition is associated with EFTUD2 p.Ser866fs (c.2595dup)?

EFTUD2 p.Ser866fs (c.2595dup) is associated with Inborn genetic diseases (ClinVar).

How common is EFTUD2 p.Ser866fs (c.2595dup) in the general population?

EFTUD2 p.Ser866fs (c.2595dup) is no gnomAD frequency available for this variant (gnomAD).

EFTUD2 p.Ser866fs

c.2595dup · rs1555563998 · VCV521038

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Inborn genetic diseases

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 haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 26 of 28
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 2.7, phastCons 1

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: EFTUD2
Protein: p.Ser866fs
Coding: c.2595dup
MANE Select: NM_004247
dbSNP: rs1555563998
Type: Duplication
Location: chr17:44852528 (GRCh38)
Gene constraint: LOEUF 0.145 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 89.94 · 72 PDB
Residue 866: a turn

Full EFTUD2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

EFTUD2 p.Arg785fs Pathogenic ★ same condition
EFTUD2 p.Ser866= Likely benign ★ same residue
EFTUD2 c.1058+1G>A Pathogenic ★★ same condition
EFTUD2 c.702+1G>T Pathogenic/Likely pathogenic ★★ same condition
EFTUD2 p.Arg354Ter Pathogenic/Likely pathogenic ★★ same condition
EFTUD2 c.2347+3A>G Uncertain significance ★★ same condition
EFTUD2 p.Arg495Gln Uncertain significance ★★ ⚠ same condition
EFTUD2 p.Arg529Cys Uncertain significance ★★ ⚠ 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/eftud2-p-ser866fs (accessed [today's date]).

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