API5 p.Arg504=
c.1512G>A · rs560522772 · VCV3127820
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.016%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| REVEL | 0.169 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | Δ0.29 | acceptor gain · deltas |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 12.78 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.016%
African / African-American · 12/74,950 alleles
Filtering AF
0.00921%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00721%
Overall
0.000807%
13/1,610,680 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.016% | 6,246 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,328 |
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
- API5
- Protein
- p.Arg504=
- Coding
- c.1512G>A
- MANE Select
- NM_001142930
- dbSNP
- rs560522772
- Type
- single nucleotide variant
- Location
- chr11:43342447 (GRCh38)
- Gene constraint
- LOEUF 0.211 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 85.04 · 3 PDB
- Residue 504
- the 'disordered' region
Similar variants
- API5 p.Ala402Thr Uncertain significance ★ ⚠ same type
- API5 p.Arg243Trp Uncertain significance ★ ⚠ same type
- API5 p.Asn517His Uncertain significance ★ ⚠ same type
- API5 p.Asp164Glu Uncertain significance ★ ⚠ same type
- API5 p.Asp359His Uncertain significance ★ ⚠ same type
- API5 p.Asp427His Uncertain significance ★ ⚠ same type
- API5 p.Cys234Tyr Uncertain significance ★ ⚠ same type
- API5 p.Glu215Gln 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/api5-p-arg504 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown