EPPK1 p.Ile1691=
c.5073C>T · rs200293863 · VCV2658932
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.171%, nfe)
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 -4.3 | GERP -3.7 |
| Overall | ||
| CADD | 5.798 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.171%
European (non-Finnish) · 2,012/1,179,982 alleles
Filtering AF
0.164%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.162%
Overall
0.139%
2,238/1,613,072 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.171% | 586 |
| Remaining individualsnot grpmax-eligible | 0.104% | 961 |
| Middle Eastern | 0.099% | 1,010 |
| Finnishnot grpmax-eligible | 0.073% | 1,369 |
| South Asian | 0.0714% | 1,401 |
| Admixed American | 0.0483% | 2,070 |
| African / African-American | 0.0186% | 5,363 |
| East Asian | 0.00223% | 44,884 |
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.Ile1691=
- Coding
- c.5073C>T
- MANE Select
- NM_031308
- dbSNP
- rs200293863
- Type
- single nucleotide variant
- Location
- chr8:143868181 (GRCh38)
- Gene constraint
- LOEUF 1.929 · pLI 0.12 (gnomAD)
- Residue 1691
- 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-ile1691 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown