Is ELAC2 p.Arg29Phe (c.85_86delinsTT) pathogenic?

ELAC2 p.Arg29Phe (c.8586delinsTT) is classified Uncertain significance in ELAC2 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-12-16). No gnomAD frequency available for this variant; Associated with combined oxidative phosphorylation defect type 17.

What condition is associated with ELAC2 p.Arg29Phe (c.85_86delinsTT)?

ELAC2 p.Arg29Phe (c.85_86delinsTT) is associated with combined oxidative phosphorylation defect type 17 (ClinVar).

How common is ELAC2 p.Arg29Phe (c.85_86delinsTT) in the general population?

ELAC2 p.Arg29Phe (c.85_86delinsTT) is no gnomAD frequency available for this variant (gnomAD).

ELAC2 p.Arg29Phe

Q: How is Combined oxidative phosphorylation defect type 17 inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

c.85_86delinsTT · rs2143697792 · VCV1466916

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

combined oxidative phosphorylation defect type 17

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 4.6	GERP -0.12, phastCons 1
Regional constraint	o/e 1.03	unconstrained · MANE · 25 kb · p 0.4 · regional, not allelic

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: ELAC2
Protein: p.Arg29Phe
Coding: c.85_86delinsTT
MANE Select: NM_018127
dbSNP: rs2143697792
Type: Indel
Location: chr17:13017862 (GRCh38)
Gene constraint: LOEUF 1.02 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 82.81 · 10 PDB
Residue 29: the 'disordered' region

Full ELAC2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

combined oxidative phosphorylation defect type 17 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Combined oxidative phosphorylation defect type 17 (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

ELAC2 p.Arg29= Likely benign ★ same residue
ELAC2 c.297-2_297-1delinsT Pathogenic/Likely pathogenic ★★ same condition
ELAC2 c.1305-8delinsCTCTC Benign/Likely benign ★★ same condition
ELAC2 p.Arg29Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
ELAC2 p.Cys374Leu Uncertain significance ★ same condition
ELAC2 p.Glu798Leu Uncertain significance ★ same condition
ELAC2 p.Gly233Lys Uncertain significance ★ same condition
ELAC2 p.Val578Leu 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/elac2-p-arg29phe (accessed [today's date]).

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