Is EFTUD2 p.Lys142fs (c.423del) pathogenic?

EFTUD2 p.Lys142fs (c.423del) is classified Pathogenic in EFTUD2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-09-22). No gnomAD frequency available for this variant; Associated with mandibulofacial dysostosis-microcephaly syndrome.

What condition is associated with EFTUD2 p.Lys142fs (c.423del)?

EFTUD2 p.Lys142fs (c.423del) is associated with mandibulofacial dysostosis-microcephaly syndrome (ClinVar).

How common is EFTUD2 p.Lys142fs (c.423del) in the general population?

EFTUD2 p.Lys142fs (c.423del) is no gnomAD frequency available for this variant (gnomAD).

EFTUD2 p.Lys142fs

c.423del · rs2508834526 · VCV1706532

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

mandibulofacial dysostosis-microcephaly syndrome

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 5 of 28
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.8	GERP 1.9, 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.Lys142fs
Coding: c.423del
MANE Select: NM_004247
dbSNP: rs2508834526
Type: Deletion
Location: chr17:44883652 (GRCh38)
Gene constraint: LOEUF 0.145 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 89.94 · 72 PDB
Residue 142: the tr-type g domain; a β-strand; a binding site

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

Disease context

mandibulofacial dysostosis-microcephaly syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

EFTUD2 c.2562-2_2562-1del Pathogenic/Likely pathogenic ★★ same condition
EFTUD2 c.2562-2del Pathogenic ★★ same condition
EFTUD2 c.702+1del Pathogenic ★★ same condition
EFTUD2 p.Leu190fs Pathogenic/Likely pathogenic ★★ same condition
EFTUD2 p.Leu474fs Pathogenic ★★ same condition
EFTUD2 p.Met433fs Pathogenic ★★ same condition
EFTUD2 c.1058+3_1058+7del Benign/Likely benign ★★ same condition
EFTUD2 c.2565del Pathogenic ★ 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-lys142fs (accessed [today's date]).

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