EGLN2 p.Pro51=
c.153A>G · rs144124916 · VCV1774789
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.02%, 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 -1.8 | |
| Overall | ||
| CADD | 3.558 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.02%
African / African-American · 15/74,932 alleles
Filtering AF
0.0123%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00989%
Overall
0.000991%
16/1,613,878 alleles · ultra-rare
exomes 4/1,461,688 · genomes 12/152,190 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.02% | 4,995 |
| Admixed American | 0.00167% | 60,000 |
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.Pro51=
- Coding
- c.153A>G
- MANE Select
- NM_080732
- dbSNP
- rs144124916
- Type
- single nucleotide variant
- Location
- chr19:40800725 (GRCh38)
- Gene constraint
- LOEUF 0.582 · pLI 0.67 (gnomAD)
- Structure
- AlphaFold pLDDT 69.05 · 1 PDB
- Residue 51
- the 'disordered' region
Similar variants
- EGLN2 p.Pro51Ala Uncertain significance ★ ⚠ same residue
- EGLN2 p.Pro51Arg Uncertain significance ★ ⚠ same residue
- EGLN2 p.Pro51Leu 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
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-pro51 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown