Is EFTUD2 p.Phe349fs (c.1044dup) pathogenic?

EFTUD2 p.Phe349fs (c.1044dup) is classified Pathogenic in EFTUD2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-10-27). Absent from gnomAD.

How common is EFTUD2 p.Phe349fs (c.1044dup) in the general population?

EFTUD2 p.Phe349fs (c.1044dup) is absent from gnomAD (gnomAD).

EFTUD2 p.Phe349fs

c.1044dup · rs2508783265 · VCV2809944

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

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 12 of 28
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 2.8, 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.Phe349fs
Coding: c.1044dup
MANE Select: NM_004247
dbSNP: rs2508783265
Type: Duplication
Location: chr17:44868300 (GRCh38)
Gene constraint: LOEUF 0.145 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 89.94 · 72 PDB
Residue 349: the tr-type g domain; a β-strand

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

Similar variants

EFTUD2 p.Phe349Val Uncertain significance ★★ ⚠ same residue
EFTUD2 p.Phe349Leu Uncertain significance ★ ⚠ same residue
EFTUD2 c.272-8dup Benign/Likely benign ★★ same type
EFTUD2 p.Ala676fs Likely pathogenic ★ same type
EFTUD2 p.Arg785fs Pathogenic ★ same type
EFTUD2 p.Arg919fs Likely pathogenic ★ same type
EFTUD2 p.Arg939fs Likely pathogenic ★ same type
EFTUD2 p.Asn548fs Likely pathogenic ★ 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/eftud2-p-phe349fs (accessed [today's date]).

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