EPN3 p.His73=
c.219C>T · VCV3509537
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0379%, eas)
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 -8.2 | GERP -1.7 |
| Overall | ||
| CADD | 4.786 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0379%
East Asian · 17/44,880 alleles
Filtering AF
0.0241%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0197%
Overall
0.00341%
55/1,614,158 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0379% | 2,640 |
| South Asian | 0.0263% | 3,795 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,502 |
| Admixed American | 0.00167% | 60,020 |
| European (non-Finnish) | 0.000678% | 147,505 |
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
- EPN3
- Protein
- p.His73=
- Coding
- c.219C>T
- MANE Select
- NM_017957
- Type
- single nucleotide variant
- Location
- chr17:50536775 (GRCh38)
- Gene constraint
- LOEUF 1.251 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 61.01
- Residue 73
- the enth domain; a binding site
Similar variants
- EPN3 p.Ala244Val Uncertain significance ★ ⚠ same type
- EPN3 p.Ala267Thr Uncertain significance ★ ⚠ same type
- EPN3 p.Ala270Gly Uncertain significance ★ ⚠ same type
- EPN3 p.Ala334Ser Uncertain significance ★ ⚠ same type
- EPN3 p.Ala334Thr Uncertain significance ★ ⚠ same type
- EPN3 p.Ala390Val Uncertain significance ★ ⚠ same type
- EPN3 p.Ala492Val Uncertain significance ★ ⚠ same type
- EPN3 p.Ala541Glu Uncertain significance ★ ⚠ 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/epn3-p-his73 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown