Is ELAC2 p.Ser710= (c.2130C>T) pathogenic?

ELAC2 p.Ser710= (c.2130C>T) is classified Benign in ELAC2 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-02-03). Common (popmax 6.89%, afr) — too common for a highly-penetrant pathogenic allele; Associated with prostate cancer, hereditary, 2.

What condition is associated with ELAC2 p.Ser710= (c.2130C>T)?

ELAC2 p.Ser710= (c.2130C>T) is associated with prostate cancer, hereditary, 2, combined oxidative phosphorylation defect type 17 (ClinVar).

How is Familial prostate cancer inherited?

Typically Not applicable (Orphanet). A genetic counselor can assess individual risk for a family.

ELAC2 p.Ser710=

Q: How common is ELAC2 p.Ser710= (c.2130C>T) in the general population?

ELAC2 p.Ser710= (c.2130C>T) is common (popmax 6.89%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.2130C>T · rs7217826 · VCV381413

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Common

common (popmax 6.89%, afr) — too common for a highly-penetrant pathogenic allele

Conditions

prostate cancer, hereditary, 2

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 -5.3	GERP -4.1
Overall
CADD	0.218	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 6.89% African / African-American · 5,170/75,028 alleles

Filtering AF 6.73% ClinGen BA1/BS1 input FAF95, joint · FAF99 6.67%

Overall 0.372% 6,011/1,614,156 alleles · common exomes 3,030/1,461,878 · genomes 2,981/152,278 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	6.89%	15
Remaining individualsnot grpmax-eligible	0.507%	197
Admixed American	0.44%	227
Middle Eastern	0.363%	276
South Asian	0.0209%	4,794
European (non-Finnish)	0.0185%	5,413
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,608

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.Ser710=
Coding: c.2130C>T
MANE Select: NM_018127
dbSNP: rs7217826
Type: single nucleotide variant
Location: chr17:12993810 (GRCh38)
Gene constraint: LOEUF 1.02 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 82.81 · 10 PDB
Residue 710: an α-helix

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

Disease context

prostate cancer, hereditary, 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: combined oxidative phosphorylation defect type 17

For Familial prostate cancer (Orphanet):

Inheritance: Not applicable
Onset: Adult
Prevalence: 1-9 / 100 000 (United States)

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-ser710 (accessed [today's date]).

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