ADD3 p.Ile668=
c.2004C>A · rs13306102 · VCV2189496
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.26%, eas)
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 | GERP -3.2, phastCons 0.002 |
| Overall | ||
| CADD | 1.797 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.26%
East Asian · 566/44,840 alleles
Filtering AF
1.18%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.14%
Overall
0.0357%
576/1,613,464 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.26% | 79 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,497 |
| South Asian | 0.0011% | 90,998 |
| European (non-Finnish) | 0.000339% | 294,917 |
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.Ile668=
- Coding
- c.2004C>A
- MANE Select
- NM_016824
- dbSNP
- rs13306102
- Type
- single nucleotide variant
- Location
- chr10:110133501 (GRCh38)
- Gene constraint
- LOEUF 0.395 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 66.83
- Residue 668
- the 'disordered' region
Similar variants
- 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
- ADD3 p.Arg645Gln Uncertain significance ★★ ⚠ same type
- ADD3 p.Asn312Asp 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-ile668 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown