AP4B1 p.Gln23=
c.69A>G · rs117872964 · VCV157726
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.5%, eas)
Conditions
2
Inborn genetic diseases
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 1.1 | GERP -0.7, phastCons 1 |
| Overall | ||
| CADD | 12.79 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.5%
East Asian · 1,571/44,862 alleles
Filtering AF
3.36%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.3%
Overall
0.102%
1,641/1,613,602 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 3.5% | 29 |
| Remaining individualsnot grpmax-eligible | 0.0608% | 1,643 |
| Middle Eastern | 0.0177% | 5,634 |
| South Asian | 0.0165% | 6,070 |
| Admixed American | 0.0117% | 8,575 |
| European (non-Finnish) | 0.000763% | 131,113 |
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
- AP4B1
- Protein
- p.Gln23=
- Coding
- c.69A>G
- MANE Select
- NM_001253852
- dbSNP
- rs117872964
- Type
- single nucleotide variant
- Location
- chr1:113904649 (GRCh38)
- Gene constraint
- LOEUF 0.777 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 86.56 · 5 PDB
Similar variants
- AP4B1 p.Gln23Lys Uncertain significance ★ ⚠ same residue
- AP4B1 c.114-2A>C Pathogenic ★★ same condition
- AP4B1 c.114-2A>G Pathogenic ★★ same condition
- AP4B1 p.Arg102Ter Pathogenic ★★ same condition
- AP4B1 p.Arg206Ter Pathogenic/Likely pathogenic ★★ same condition
- AP4B1 p.Arg353Ter Pathogenic/Likely pathogenic ★★ same condition
- AP4B1 p.Arg393Ter Pathogenic ★★ same condition
- AP4B1 p.Arg406Ter Pathogenic/Likely pathogenic ★★ 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/ap4b1-p-gln23 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown