AP4E1 p.Ser237=
c.711A>T · rs797045247 · VCV210205
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
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 -0.15 | GERP -3.5, phastCons 0.005 |
| Overall | ||
| CADD | 0.93 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,062 alleles
Overall
0.000124%
2/1,614,148 alleles · ultra-rare
exomes 2/1,461,828 · genomes 0/152,320 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,062 |
| South Asian | 0.0011% | 91,086 |
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
- AP4E1
- Protein
- p.Ser237=
- Coding
- c.711A>T
- MANE Select
- NM_007347
- dbSNP
- rs797045247
- Type
- single nucleotide variant
- Location
- chr15:50930813 (GRCh38)
- Gene constraint
- LOEUF 0.576 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.42 · 4 PDB
Similar variants
- AP4E1 p.Arg1105Ter Pathogenic ★★ same type
- AP4E1 p.Arg304Ter Pathogenic/Likely pathogenic ★★ same type
- AP4E1 p.Ala119Ser Uncertain significance ★★ ⚠ same type
- AP4E1 p.Ala45Thr Uncertain significance ★★ ⚠ same type
- AP4E1 p.Ala475Val Uncertain significance ★★ ⚠ same type
- AP4E1 p.Ala65Val Uncertain significance ★★ ⚠ same type
- AP4E1 p.Ala678Val Uncertain significance ★★ ⚠ same type
- AP4E1 p.Arg304Gln 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/ap4e1-p-ser237 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown