APBB1 p.His480=
c.1440C>T · rs188642100 · VCV773807
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.51%, eas)
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 5 | GERP -3.9, phastCons 1 |
| Overall | ||
| CADD | 11.61 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.51%
East Asian · 679/44,886 alleles
Filtering AF
1.42%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.38%
Overall
0.0583%
941/1,614,200 alleles · low-frequency
exomes 824/1,461,886 · genomes 117/152,314 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.51% | 66 |
| South Asian | 0.132% | 759 |
| Remaining individualsnot grpmax-eligible | 0.101% | 992 |
| African / African-American | 0.0227% | 4,414 |
| European (non-Finnish) | 0.00508% | 19,667 |
| Admixed American | 0.00333% | 30,011 |
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.His480=
- Coding
- c.1440C>T
- MANE Select
- NM_001164
- dbSNP
- rs188642100
- Type
- single nucleotide variant
- Location
- chr11:6401637 (GRCh38)
- Gene constraint
- LOEUF 0.401 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 60.75 · 11 PDB
- Residue 480
- the pid 1 domain; a β-strand
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.Leu385= 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
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-his480 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown