Is EGLN2 p.Ser3= (c.9C>T) pathogenic?

EGLN2 p.Ser3= (c.9C>T) is classified Likely benign in EGLN2 (ClinVar, Single submitter, 1 submitter; last evaluated 2020-08-21). Very rare (popmax 0.00669%, afr).

How common is EGLN2 p.Ser3= (c.9C>T) in the general population?

EGLN2 p.Ser3= (c.9C>T) is very rare (popmax 0.00669%, afr) (gnomAD).

EGLN2 p.Ser3=

c.9C>T · rs892202419 · VCV1768922

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00669%, afr)

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 4	phastCons 1
Overall
CADD	14.01	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00669% African / African-American · 5/74,706 alleles

Filtering AF 0.00255% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00162%

Overall 0.000375% 6/1,599,230 alleles · very rare exomes 3/1,447,084 · genomes 3/152,146 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00669%	14,941
Finnishnot grpmax-eligible	0.00162%	61,798

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: EGLN2
Protein: p.Ser3=
Coding: c.9C>T
MANE Select: NM_080732
dbSNP: rs892202419
Type: single nucleotide variant
Location: chr19:40800581 (GRCh38)
Gene constraint: LOEUF 0.582 · pLI 0.67 (gnomAD)
Structure: AlphaFold pLDDT 69.05 · 1 PDB
Residue 3: the 'disordered' region

Full EGLN2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

EGLN2 p.Ser3Gly Uncertain significance ★ ⚠ same residue
EGLN2 p.Ala137Thr Uncertain significance ★★ ⚠ same type
EGLN2 p.Arg236Cys Uncertain significance ★★ ⚠ same type
EGLN2 p.Arg306Cys Uncertain significance ★★ ⚠ same type
EGLN2 c.1100+23C>A Benign ★★ same type
EGLN2 c.844-141G>A Benign ★★ same type
EGLN2 c.844-199G>A Benign ★★ same type
EGLN2 c.963+33G>C Benign ★★ same type

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/egln2-p-ser3 (accessed [today's date]).

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