EGLN2 p.Pro75=
c.225T>G · rs759874407 · VCV2560613
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, sas)
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 -0.14 | phastCons 0.01 |
| Overall | ||
| CADD | 3.628 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
South Asian · 15/91,052 alleles
Filtering AF
0.0101%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00811%
Overall
0.00105%
17/1,613,510 alleles · ultra-rare
exomes 17/1,461,218 · genomes 0/152,292 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0165% | 6,070 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,242 |
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.Pro75=
- Coding
- c.225T>G
- MANE Select
- NM_080732
- dbSNP
- rs759874407
- Type
- single nucleotide variant
- Location
- chr19:40800797 (GRCh38)
- Gene constraint
- LOEUF 0.582 · pLI 0.67 (gnomAD)
- Structure
- AlphaFold pLDDT 69.05 · 1 PDB
- Residue 75
- the 'disordered' region
Similar variants
- EGLN2 p.Pro75Arg 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-pro75 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown