EPOR c.252-257del
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 16.3%, eas) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | acceptor -257 | deep intronic (-257 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -0.75 | GERP -0.48, phastCons 0.001 |
| Non-coding constraint | Z 3.32 | 1 kb window · o/e 0.78 · regional · uncalibrated |
| Overall | ||
| CADD | 0.896 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
16.3%
East Asian · 720/4,418 alleles
Filtering AF
15.3%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 14.9%
Overall
6.27%
7,816/124,746 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 16.3% | 6 |
| African / African-American | 7.36% | 14 |
| Finnishnot grpmax-eligible | 6.35% | 16 |
| European (non-Finnish) | 5.86% | 17 |
| Remaining individualsnot grpmax-eligible | 5.65% | 18 |
| South Asian | 5.63% | 18 |
| Admixed American | 3.64% | 28 |
| Amishnot grpmax-eligible | 2.27% | 44 |
| Middle Eastern | 2.23% | 45 |
| Ashkenazi Jewishnot grpmax-eligible | 1.4% | 71 |
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
- EPOR
- Coding
- c.252-257del
- MANE Select
- NM_000121
- dbSNP
- rs869111819
- Type
- Deletion
- Location
- chr19:11382362 (GRCh38)
- Gene constraint
- LOEUF 0.787 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 67.74 · 22 PDB
Similar variants
- EPOR p.Leu493fs Uncertain significance ★ same type
- EPOR p.Pro438fs 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/epor-c-252-minus-257del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown