EPPK1 p.Ala1496=
c.4488G>A · rs114155737 · VCV3035625
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 4.31%, afr)
Conditions
1
EPPK1-related disorder
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 -20 | GERP -3.4 |
| Overall | ||
| CADD | 0.042 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.31%
African / African-American · 3,218/74,698 alleles
Filtering AF
4.18%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.13%
Overall
0.23%
3,668/1,593,526 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.31% | 23 |
| Middle Eastern | 0.33% | 303 |
| Remaining individualsnot grpmax-eligible | 0.229% | 437 |
| Admixed American | 0.165% | 605 |
| European (non-Finnish) | 0.0153% | 6,529 |
| East Asian | 0.00905% | 11,046 |
| South Asian | 0.00672% | 14,890 |
| Finnishnot grpmax-eligible | 0.00372% | 26,872 |
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.Ala1496=
- Coding
- c.4488G>A
- MANE Select
- NM_031308
- dbSNP
- rs114155737
- Type
- single nucleotide variant
- Location
- chr8:143868766 (GRCh38)
- Gene constraint
- LOEUF 1.929 · pLI 0.12 (gnomAD)
Disease context
EPPK1-related disorder
Similar variants
- EPPK1 p.Gln2020Arg Uncertain significance ★ ⚠ same condition
- EPPK1 p.Glu140Ter Uncertain significance ★ same condition
- EPPK1 p.Pro35Thr Uncertain significance ★ ⚠ same condition
- EPPK1 p.Val104Leu Uncertain significance ★ ⚠ same condition
- EPPK1 p.Ala2265= Likely benign ★ same condition
- EPPK1 p.Arg2218= Likely benign ★ same condition
- EPPK1 p.Arg2305= Likely benign ★ same condition
- EPPK1 p.Arg2356= Likely benign ★ same condition
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-ala1496 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown