Is ELAC2 p.Ser52= (c.156C>T) pathogenic?

ELAC2 p.Ser52= (c.156C>T) is classified Likely benign in ELAC2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-26). Ultra-rare (popmax 0.024%, afr); Associated with combined oxidative phosphorylation defect type 17.

What condition is associated with ELAC2 p.Ser52= (c.156C>T)?

ELAC2 p.Ser52= (c.156C>T) is associated with combined oxidative phosphorylation defect type 17 (ClinVar).

How common is ELAC2 p.Ser52= (c.156C>T) in the general population?

ELAC2 p.Ser52= (c.156C>T) is ultra-rare (popmax 0.024%, afr) (gnomAD).

ELAC2 p.Ser52=

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.156C>T · rs375941310 · VCV1088721

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.024%, afr)

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 · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.65	GERP -4
Overall
CADD	3.678	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.024% African / African-American · 18/74,874 alleles

Filtering AF 0.0155% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0128%

Overall 0.00274% 44/1,607,748 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.024%	4,160
East Asian	0.00448%	22,335
Admixed American	0.00337%	29,669
Remaining individualsnot grpmax-eligible	0.00322%	31,079
European (non-Finnish)	0.0017%	58,897

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: ELAC2
Protein: p.Ser52=
Coding: c.156C>T
MANE Select: NM_018127
dbSNP: rs375941310
Type: single nucleotide variant
Location: chr17:13017792 (GRCh38)
Gene constraint: LOEUF 1.02 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 82.81 · 10 PDB
Residue 52: a UniProt-annotated variant site (in)

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.Ser52Phe Likely benign ★★ ⚠ same residue
ELAC2 p.Ser52Cys Conflicting classifications of pathogenicity ★ ⚠ same residue
ELAC2 p.Ser52Pro Uncertain significance ★ ⚠ same residue
ELAC2 p.Ser52Tyr Uncertain significance ★ ⚠ same residue
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

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-ser52 (accessed [today's date]).

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