AP3B2 p.Glu103=
c.309G>A · rs142080998 · VCV731248
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.43%, eas)
Conditions
1
developmental and epileptic encephalopathy, 48
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 -0.3 | GERP -3.8, phastCons 0.16 |
| Overall | ||
| CADD | 8.394 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.43%
East Asian · 642/44,866 alleles
Filtering AF
1.34%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.3%
Overall
0.0448%
722/1,613,122 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.43% | 70 |
| South Asian | 0.0408% | 2,453 |
| Remaining individualsnot grpmax-eligible | 0.0384% | 2,602 |
| African / African-American | 0.0187% | 5,359 |
| Admixed American | 0.00167% | 59,890 |
| European (non-Finnish) | 0.000339% | 294,894 |
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
- AP3B2
- Protein
- p.Glu103=
- Coding
- c.309G>A
- MANE Select
- NM_001278512
- dbSNP
- rs142080998
- Type
- single nucleotide variant
- Location
- chr15:82688787 (GRCh38)
- Gene constraint
- LOEUF 0.52 · pLI 0.22 (gnomAD)
- Structure
- AlphaFold pLDDT 75.73
Similar variants
- AP3B2 p.Arg977Ter Pathogenic ★★ same condition
- AP3B2 p.Gln839Ter Pathogenic/Likely pathogenic ★★ same condition
- AP3B2 c.1110+3G>C Uncertain significance ★★ same condition
- AP3B2 p.Ala1098Asp Uncertain significance ★★ ⚠ same condition
- AP3B2 p.Ala546Pro Uncertain significance ★★ ⚠ same condition
- AP3B2 p.Arg977Gln Uncertain significance ★★ ⚠ same condition
- AP3B2 p.Arg99Cys Uncertain significance ★★ ⚠ same condition
- AP3B2 p.Asn552Tyr Uncertain significance ★★ ⚠ 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/ap3b2-p-glu103 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown