ADD3 p.Asp587=
c.1761C>T · rs575167097 · VCV2978139
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.016%, 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 -0.22 | GERP 0.31, phastCons 0.22 |
| Overall | ||
| CADD | 11.03 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.016%
African / African-American · 12/74,882 alleles
Filtering AF
0.00922%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00722%
Overall
0.00242%
39/1,613,368 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.016% | 6,240 |
| East Asian | 0.0134% | 7,480 |
| Admixed American | 0.00334% | 29,980 |
| Finnishnot grpmax-eligible | 0.00313% | 31,989 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,464 |
| European (non-Finnish) | 0.00136% | 73,722 |
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
- ADD3
- Protein
- p.Asp587=
- Coding
- c.1761C>T
- MANE Select
- NM_016824
- dbSNP
- rs575167097
- Type
- single nucleotide variant
- Location
- chr10:110132333 (GRCh38)
- Gene constraint
- LOEUF 0.395 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 66.83
- Residue 587
- the 'disordered' region
Similar variants
- ADD3 p.Asp587Gly Uncertain significance ★★ ⚠ same residue
- ADD3 p.Asp587Val Uncertain significance ★ ⚠ same residue
- ADD3 p.Gly367Asp Pathogenic/Likely pathogenic ★★ same type
- ADD3 c.1733-1G>A Uncertain significance ★★ same type
- ADD3 p.Ala588Gly Uncertain significance ★★ ⚠ same type
- ADD3 p.Arg27Cys Uncertain significance ★★ ⚠ same type
- ADD3 p.Arg46Gln Uncertain significance ★★ ⚠ same type
- ADD3 p.Arg571His 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/add3-p-asp587 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown