EPPK1 p.Pro789=
c.2367C>T · rs200117350 · VCV2658937
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0913%, eas)
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 -7.3 | GERP -3.7 |
| Overall | ||
| CADD | 1.865 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0913%
East Asian · 41/44,900 alleles
Filtering AF
0.0692%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0614%
Overall
0.00539%
87/1,613,060 alleles · ultra-rare
exomes 73/1,460,854 · genomes 14/152,206 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0913% | 1,095 |
| Remaining individualsnot grpmax-eligible | 0.0608% | 1,644 |
| African / African-American | 0.00267% | 37,464 |
| European (non-Finnish) | 0.000508% | 196,665 |
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
- EPPK1
- Protein
- p.Pro789=
- Coding
- c.2367C>T
- MANE Select
- NM_031308
- dbSNP
- rs200117350
- Type
- single nucleotide variant
- Location
- chr8:143870887 (GRCh38)
- Gene constraint
- LOEUF 1.929 · pLI 0.12 (gnomAD)
- Residue 789
- the 'interaction with krt5' region
Similar variants
- EPPK1 p.Gly716Ser Uncertain significance ★★ same type
- EPPK1 p.Gly441Ser Benign/Likely benign ★★ same type
- EPPK1 p.Ala1025Thr Uncertain significance ★ same type
- EPPK1 p.Ala1076Val Uncertain significance ★ ⚠ same type
- EPPK1 p.Ala1119Val Uncertain significance ★ ⚠ same type
- EPPK1 p.Ala1138Val Uncertain significance ★ ⚠ same type
- EPPK1 p.Ala118Thr Uncertain significance ★ same type
- EPPK1 p.Ala1205Thr 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/eppk1-p-pro789 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown