EPPK1 p.Thr2153=
c.6459G>A · rs114125680 · VCV2658925
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.281%, 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 -4.8 | GERP -3.4 |
| Overall | ||
| CADD | 0.686 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.281%
European (non-Finnish) · 3,321/1,179,870 alleles
Filtering AF
0.273%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.27%
Overall
0.239%
3,852/1,613,474 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.281% | 355 |
| Remaining individualsnot grpmax-eligible | 0.227% | 440 |
| African / African-American | 0.211% | 475 |
| Admixed American | 0.165% | 606 |
| Finnishnot grpmax-eligible | 0.161% | 623 |
| East Asian | 0.0446% | 2,244 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0169% | 5,921 |
| South Asian | 0.00549% | 18,218 |
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.Thr2153=
- Coding
- c.6459G>A
- MANE Select
- NM_031308
- dbSNP
- rs114125680
- Type
- single nucleotide variant
- Location
- chr8:143866795 (GRCh38)
- Gene constraint
- LOEUF 1.929 · pLI 0.12 (gnomAD)
- Residue 2153
- the 'interaction with krt5' region
Similar variants
- EPPK1 p.Thr2153Met Uncertain significance ★ ⚠ same residue
- 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
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-thr2153 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown