EPG5 p.Phe1900=
c.5700T>C · rs34545102 · VCV466259
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.2%, afr)
Conditions
1
Vici syndrome
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 3 | GERP 0.053, phastCons 1 |
| Overall | ||
| CADD | 7.126 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.2%
African / African-American · 3,149/74,942 alleles
Filtering AF
4.08%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.03%
Overall
0.235%
3,798/1,613,714 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.2% | 24 |
| Remaining individualsnot grpmax-eligible | 0.378% | 265 |
| Admixed American | 0.352% | 284 |
| Middle Eastern | 0.331% | 302 |
| European (non-Finnish) | 0.0149% | 6,704 |
| South Asian | 0.00659% | 15,172 |
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
- EPG5
- Protein
- p.Phe1900=
- Coding
- c.5700T>C
- MANE Select
- NM_020964
- dbSNP
- rs34545102
- Type
- single nucleotide variant
- Location
- chr18:45879182 (GRCh38)
- Gene constraint
- LOEUF 0.58 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.24 · 1 PDB
- Residue 1900
- a UniProt-annotated variant site (in vicis); a UniProt-annotated variant site (in nedpam)
Similar variants
- EPG5 p.Phe1900Leu Uncertain significance ★ ⚠ same residue
- EPG5 p.Phe1900Cys Uncertain significance ★ ⚠ same residue
- EPG5 c.1253-1G>A Pathogenic ★★ same condition
- EPG5 c.1497+1G>T Pathogenic/Likely pathogenic ★★ same condition
- EPG5 c.1678-1G>A Likely pathogenic ★★ same condition
- EPG5 c.4475-1G>A Likely pathogenic ★★ same condition
- EPG5 c.5304+1G>A Likely pathogenic ★★ same condition
- EPG5 c.5869+1G>A Pathogenic ★★ 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/epg5-p-phe1900 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown