ADAT3 p.Ala196Val
c.587C>T · VCV4086440
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0181%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.257 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 4.5 | GERP 1.4, phastCons 1 |
| Regional constraint | o/e 1.29 | unconstrained · MANE · 1,100 bp · p 7.8e-12 · regional, not allelic |
| Overall | ||
| CADD | 25.4 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0181%
Admixed American · 6/33,098 alleles
Filtering AF
0.00789%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00535%
Overall
0.00425%
61/1,436,698 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0181% | 5,516 |
| European (non-Finnish) | 0.00453% | 22,081 |
| Remaining individualsnot grpmax-eligible | 0.00363% | 27,531 |
| African / African-American | 0.00301% | 33,172 |
| Finnishnot grpmax-eligible | 0.00235% | 42,608 |
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
- ADAT3
- Protein
- p.Ala196Val
- Coding
- c.587C>T
- MANE Select
- NM_138422
- Type
- single nucleotide variant
- Location
- chr19:1912634 (GRCh38)
- Gene constraint
- LOEUF 1.929 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.83
- Residue 196
- the cmp/dcmp-type deaminase domain
Similar variants
- ADAT3 p.Ala196fs Conflicting classifications of pathogenicity ★ same residue
- ADAT3 p.Ala196Leu Uncertain significance ★ same residue
- ADAT3 p.Val144Met Pathogenic/Likely pathogenic ★★ same type
- ADAT3 p.Ala20Val Uncertain significance ★★ same type
- ADAT3 p.Arg209Gln Uncertain significance ★★ same type
- ADAT3 p.Arg250Cys Uncertain significance ★★ same type
- ADAT3 p.Asp330Asn Uncertain significance ★★ same type
- ADAT3 p.Gly251Ser 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/adat3-p-ala196val (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown