ADD2 p.Val602=
c.1806G>A · rs782535457 · VCV3082792
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0713%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.058 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.6 | GERP -5 |
| Overall | ||
| CADD | 2.635 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0713%
East Asian · 32/44,866 alleles
Filtering AF
0.0519%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0452%
Overall
0.00204%
33/1,613,862 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0713% | 1,402 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,504 |
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
- ADD2
- Protein
- p.Val602=
- Coding
- c.1806G>A
- MANE Select
- NM_001617
- dbSNP
- rs782535457
- Type
- single nucleotide variant
- Location
- chr2:70672942 (GRCh38)
- Gene constraint
- LOEUF 0.388 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 66.51
- Residue 602
- the 'disordered' region
Similar variants
- ADD2 p.Asp28Asn Benign ★★ ⚠ same type
- ADD2 p.Glu335Asp Benign ★★ same type
- ADD2 p.Gly17Glu Benign ★★ same type
- ADD2 p.Ala150Val Uncertain significance ★ ⚠ same type
- ADD2 p.Ala232Gly Uncertain significance ★ ⚠ same type
- ADD2 p.Ala312Thr Uncertain significance ★ ⚠ same type
- ADD2 p.Ala418Pro Uncertain significance ★ ⚠ same type
- ADD2 p.Ala606Val 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/add2-p-val602 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown