Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.49%, 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 8.7 | GERP 1.8, phastCons 1 |
| Overall | ||
| CADD | 11.31 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.49%
African / African-American · 1,118/75,040 alleles
Filtering AF
1.42%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.39%
Overall
0.0772%
1,246/1,614,164 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.49% | 67 |
| Middle Eastern | 0.148% | 674 |
| Remaining individualsnot grpmax-eligible | 0.0928% | 1,078 |
| Admixed American | 0.0616% | 1,622 |
| South Asian | 0.00439% | 22,769 |
| European (non-Finnish) | 0.00169% | 59,001 |
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.Leu385=
- Coding
- c.1153C>T
- MANE Select
- NM_001164
- dbSNP
- rs1800424
- Type
- single nucleotide variant
- Location
- chr11:6402677 (GRCh38)
- Gene constraint
- LOEUF 0.401 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 60.75 · 11 PDB
- Residue 385
- the pid 1 domain; an α-helix
Similar variants
- SMPD1 p.Arg498Leu Pathogenic ★★ same type
- APBB1 p.Ala371= Benign ★★ same type
- APBB1 p.Arg51Cys Benign ★★ ⚠ same type
- APBB1 p.Asn126= Benign ★★ same type
- APBB1 p.Met327Val Likely benign ★★ same type
- APBB1 c.721+1G>T Uncertain significance ★ same type
- APBB1 p.Ala157Val Uncertain significance ★ ⚠ same type
- APBB1 p.Ala194Asp 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/apbb1-p-leu385 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown