DRAP1 p.Arg16=
c.48G>A · rs149754486 · VCV710012
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 2.38%, 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 1.6 | GERP -2.1, phastCons 1 |
| Overall | ||
| CADD | 10.77 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.38%
African / African-American · 1,790/75,064 alleles
Filtering AF
2.29%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.26%
Overall
0.123%
1,987/1,613,014 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.38% | 42 |
| Remaining individualsnot grpmax-eligible | 0.141% | 710 |
| Admixed American | 0.135% | 741 |
| South Asian | 0.00659% | 15,180 |
| European (non-Finnish) | 0.00186% | 53,635 |
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
- DRAP1
- Protein
- p.Arg16=
- Coding
- c.48G>A
- MANE Select
- NM_006442
- dbSNP
- rs149754486
- Type
- single nucleotide variant
- Location
- chr11:65919785 (GRCh38)
- Gene constraint
- LOEUF 0.738 · pLI 0.18 (gnomAD)
- Structure
- AlphaFold pLDDT 73.87 · 1 PDB
- Residue 16
- an α-helix; the histone-fold domain
Similar variants
- DRAP1 p.Arg109Cys Uncertain significance ★ ⚠ same type
- DRAP1 p.Arg112Trp Uncertain significance ★ ⚠ same type
- DRAP1 p.Asn100Asp Uncertain significance ★ ⚠ same type
- DRAP1 p.Asp105His Uncertain significance ★ ⚠ same type
- DRAP1 p.Asp130Glu Uncertain significance ★ ⚠ same type
- DRAP1 p.Asp196Asn Uncertain significance ★ ⚠ same type
- DRAP1 p.Gln55His Uncertain significance ★ ⚠ same type
- DRAP1 p.Glu198Asp 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/drap1-p-arg16 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown