ADD3 p.Ile658=
c.1974C>T · rs568629103 · VCV3016258
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00446%, 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 0.23 | GERP 2.1, phastCons 0.98 |
| Overall | ||
| CADD | 9.679 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00446%
East Asian · 2/44,856 alleles
Filtering AF
0.00106%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000495%
Overall
0.000372%
6/1,613,800 alleles · very rare
exomes 4/1,461,620 · genomes 2/152,180 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00446% | 22,428 |
| African / African-American | 0.004% | 24,997 |
| South Asian | 0.0011% | 91,060 |
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.Ile658=
- Coding
- c.1974C>T
- MANE Select
- NM_016824
- dbSNP
- rs568629103
- Type
- single nucleotide variant
- Location
- chr10:110133471 (GRCh38)
- Gene constraint
- LOEUF 0.395 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 66.83
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-ile658 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown