Is ELAC2 p.Ser52Pro (c.154T>C) pathogenic?

ELAC2 p.Ser52Pro (c.154T>C) is classified Uncertain significance in ELAC2 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-08-31). AlphaMissense: likely benign (0.0601); Very rare (popmax 0.00443%, sas); Associated with combined oxidative phosphorylation defect type 17.

What condition is associated with ELAC2 p.Ser52Pro (c.154T>C)?

ELAC2 p.Ser52Pro (c.154T>C) is associated with combined oxidative phosphorylation defect type 17 (ClinVar).

How common is ELAC2 p.Ser52Pro (c.154T>C) in the general population?

ELAC2 p.Ser52Pro (c.154T>C) is very rare (popmax 0.00443%, sas) (gnomAD).

What do computational predictors say about ELAC2 p.Ser52Pro (c.154T>C)?

AlphaMissense predicts likely benign (score 0.0601) — an in-silico prediction, not a clinical call.

ELAC2 p.Ser52Pro

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.154T>C · rs755823018 · VCV841174

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0601 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00443%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

combined oxidative phosphorylation defect type 17

Computational evidence

Protein change
AlphaMissense	0.0601	likely benign
REVEL	0.047	moderately benign-leaning
SaProt	LLR -6.16	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2	GERP -1.2, phastCons 0.97
Regional constraint	o/e 1.03	unconstrained · MANE · 25 kb · p 0.4 · regional, not allelic
Overall
CADD	10.56	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00443% South Asian · 4/90,358 alleles

Filtering AF 0.00143% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000897%

Overall 0.000373% 6/1,607,974 alleles · very rare exomes 6/1,455,666 · genomes 0/152,308 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00443%	22,589
East Asian	0.00224%	44,680
European (non-Finnish)	8.49e-05%	1,177,992

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.Ser52Pro
Coding: c.154T>C
MANE Select: NM_018127
dbSNP: rs755823018
Type: single nucleotide variant
Location: chr17:13017794 (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.Ser52Tyr Uncertain significance ★ ⚠ same residue
ELAC2 p.Ser52= Likely benign ★ 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-ser52pro (accessed [today's date]).

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