ACP4 p.Pro46=
c.138G>A · rs200405470 · VCV3052299
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.259%, sas)
Conditions
1
ACP4-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 -9.3 | GERP -3.9 |
| Overall | ||
| CADD | 0.849 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.259%
South Asian · 218/84,262 alleles
Filtering AF
0.231%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.22%
Overall
0.0218%
339/1,551,734 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.259% | 387 |
| Middle Eastern | 0.201% | 496 |
| Remaining individualsnot grpmax-eligible | 0.0299% | 3,345 |
| Admixed American | 0.0252% | 3,966 |
| East Asian | 0.0097% | 10,313 |
| European (non-Finnish) | 0.00644% | 15,525 |
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
- ACP4
- Protein
- p.Pro46=
- Coding
- c.138G>A
- MANE Select
- NM_033068
- dbSNP
- rs200405470
- Type
- single nucleotide variant
- Location
- chr19:50790620 (GRCh38)
- Gene constraint
- LOEUF 1.413 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.30
Disease context
ACP4-related disorder
Similar variants
- ACP4 p.Pro46Leu Uncertain significance ★ ⚠ same residue
- ACP4 c.1165+2T>G Likely benign same condition
- ACP4 c.549+7A>G Likely benign same condition
- ACP4 p.Ala121= Likely benign same condition
- ACP4 p.Ala325Asp Benign same condition
- ACP4 p.Ala325Thr Benign same condition
- ACP4 p.His218= Likely benign same condition
- ACP4 p.Pro155= Likely benign 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/acp4-p-pro46 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown