Is ELAC2 p.Thr631= (c.1893A>G) pathogenic?

ELAC2 p.Thr631= (c.1893A>G) is classified Benign in ELAC2 (ClinVar, Multiple submitters, 7 submitters; last evaluated 2026-02-04). Common (popmax 20.5%, mid) — too common for a highly-penetrant pathogenic allele; Associated with combined oxidative phosphorylation defect type 17.

ELAC2 p.Thr631=

Q: What condition is associated with ELAC2 p.Thr631= (c.1893A>G)?

ELAC2 p.Thr631= (c.1893A>G) is associated with combined oxidative phosphorylation defect type 17, prostate cancer, hereditary, 2 (ClinVar).

Q: How common is ELAC2 p.Thr631= (c.1893A>G) in the general population?

ELAC2 p.Thr631= (c.1893A>G) is common (popmax 20.5%, mid) — too common for a highly-penetrant pathogenic allele (gnomAD).

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.1893A>G · rs17552022 · VCV380022

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 7 submitters

gnomAD v4.1

Common

common (popmax 20.5%, mid) — too common for a highly-penetrant pathogenic allele

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 -5.5	GERP -4.2
Overall
CADD	0.095	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 20.5% Middle Eastern · 1,243/6,062 alleles

Filtering AF 19.6% ClinGen BA1/BS1 input FAF95, joint · FAF99 19.2%

Overall 11.3% 182,203/1,614,118 alleles · common

Ancestry group	Frequency	1 in
Amishnot grpmax-eligible	26.6%	4
Middle Easterngrpmax	20.5%	5
Ashkenazi Jewishnot grpmax-eligible	19.1%	5
European (non-Finnish)	12.4%	8
Remaining individualsnot grpmax-eligible	11.7%	9
South Asian	11.6%	9
Finnishnot grpmax-eligible	8.23%	12
Admixed American	6.59%	15
African / African-American	2.16%	46
East Asian	0.049%	2,040

Amish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Thr631=
Coding: c.1893A>G
MANE Select: NM_018127
dbSNP: rs17552022
Type: single nucleotide variant
Location: chr17:12994978 (GRCh38)
Gene constraint: LOEUF 1.02 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 82.81 · 10 PDB
Residue 631: an α-helix

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

Also linked: prostate cancer, hereditary, 2

For 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-thr631 (accessed [today's date]).

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