EGLN2 p.Pro174=
c.522C>T · rs551623860 · VCV1746202
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.278%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -11 | |
| Overall | ||
| CADD | 0.849 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.278%
South Asian · 253/91,088 alleles
Filtering AF
0.25%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.239%
Overall
0.0172%
278/1,612,716 alleles · rare
exomes 261/1,460,342 · genomes 17/152,374 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.278% | 360 |
| Middle Eastern | 0.0165% | 6,060 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,414 |
| African / African-American | 0.00666% | 15,013 |
| Admixed American | 0.00333% | 30,017 |
| East Asian | 0.00223% | 44,884 |
| European (non-Finnish) | 0.000848% | 117,994 |
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.Pro174=
- Coding
- c.522C>T
- MANE Select
- NM_080732
- dbSNP
- rs551623860
- Type
- single nucleotide variant
- Location
- chr19:40801094 (GRCh38)
- Gene constraint
- LOEUF 0.582 · pLI 0.67 (gnomAD)
- Structure
- AlphaFold pLDDT 69.05 · 1 PDB
- Residue 174
- an α-helix
Similar variants
- 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
- EGLN2 c.-116G>A 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-pro174 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown