ELAC2 p.Val307=
c.921G>C · rs2508306556 · VCV2692934
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
combined oxidative phosphorylation defect type 17
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.016 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>T here scores Δ0.38 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP -3.3 | GERP -4.2 |
| Overall | ||
| CADD | 0.54 | PHRED · no single calibrated threshold — expert panels disagree |
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
- ELAC2
- Protein
- p.Val307=
- Coding
- c.921G>C
- MANE Select
- NM_018127
- dbSNP
- rs2508306556
- Type
- single nucleotide variant
- Location
- chr17:13005051 (GRCh38)
- Gene constraint
- LOEUF 1.02 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.81 · 10 PDB
- Residue 307
- a β-strand
Disease context
combined oxidative phosphorylation defect type 17 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Combined oxidative phosphorylation defect type 17 (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Infancy, Neonatal
Similar variants
- ELAC2 c.1080-1G>C Likely pathogenic ★★ same condition
- ELAC2 c.1423+1G>A Pathogenic ★★ same condition
- ELAC2 c.1908+1G>A Likely pathogenic ★★ same condition
- ELAC2 c.245+2T>A Pathogenic/Likely pathogenic ★★ same condition
- ELAC2 p.Arg497Ter Pathogenic/Likely pathogenic ★★ same condition
- ELAC2 p.Gln18Ter Pathogenic ★★ same condition
- ELAC2 p.Glu30Ter Pathogenic/Likely pathogenic ★★ same condition
- ELAC2 p.Glu482Ter Pathogenic/Likely 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/elac2-p-val307 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown