APBB1 p.Ser123=
c.369A>C · rs1848948767 · VCV3046282
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000169%, nfe)
Conditions
1
APBB1-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 -8.4 | GERP -3.3 |
| Overall | ||
| CADD | 0.098 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000169%
European (non-Finnish) · 2/1,180,030 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000137%
2/1,461,850 alleles · very rare
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
- APBB1
- Protein
- p.Ser123=
- Coding
- c.369A>C
- MANE Select
- NM_001164
- dbSNP
- rs1848948767
- Type
- single nucleotide variant
- Location
- chr11:6410979 (GRCh38)
- Gene constraint
- LOEUF 0.401 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 60.75 · 11 PDB
Disease context
APBB1-related disorder
Similar variants
- SMPD1 p.Arg498Leu Pathogenic ★★ same condition
- APBB1 p.Asn396Ser Likely benign ⚠ same condition
- APBB1 p.Asp163Glu Likely benign same condition
- APBB1 p.Met412Val Likely benign same condition
- SMPD1 p.Arg610del Pathogenic ★★ same condition
- APBB1 p.Ala371= Benign ★★ same type
- APBB1 p.Arg51Cys Benign ★★ ⚠ same type
- APBB1 p.Asn126= Benign ★★ 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/apbb1-p-ser123 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown