EPC2 p.Phe6=
c.18C>T · rs189332039 · VCV783120
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.2%, afr)
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 7.4 | GERP 4.2, phastCons 1 |
| Overall | ||
| CADD | 15.49 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.2%
African / African-American · 1,611/73,202 alleles
Filtering AF
2.11%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.08%
Overall
0.116%
1,804/1,551,198 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.2% | 45 |
| Admixed American | 0.152% | 659 |
| Remaining individualsnot grpmax-eligible | 0.133% | 749 |
| Middle Eastern | 0.0503% | 1,987 |
| South Asian | 0.00355% | 28,187 |
| European (non-Finnish) | 0.00253% | 39,514 |
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
- EPC2
- Protein
- p.Phe6=
- Coding
- c.18C>T
- MANE Select
- NM_015630
- dbSNP
- rs189332039
- Type
- single nucleotide variant
- Location
- chr2:148645035 (GRCh38)
- Gene constraint
- LOEUF 0.203 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 58.35
Similar variants
- EPC2 c.666+9C>T Benign ★★ same type
- EPC2 p.Arg253= Benign ★★ same type
- EPC2 p.Ser611= Benign ★★ same type
- EPC2 p.Ala13Thr Uncertain significance ★ ⚠ same type
- EPC2 p.Ala14Asp Uncertain significance ★ ⚠ same type
- EPC2 p.Ala634Thr Uncertain significance ★ ⚠ same type
- EPC2 p.Ala711Thr Uncertain significance ★ ⚠ same type
- EPC2 p.Ala711Val 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/epc2-p-phe6 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown