ADAT3 p.Pro39=
c.117G>A · rs199915192 · VCV718244
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.648%, nfe)
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 -11 | GERP -2.5 |
| Overall | ||
| CADD | 0.108 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.648%
European (non-Finnish) · 7,544/1,164,086 alleles
Filtering AF
0.636%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.631%
Overall
0.522%
8,202/1,572,282 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.648% | 154 |
| Remaining individualsnot grpmax-eligible | 0.46% | 218 |
| Ashkenazi Jewishnot grpmax-eligible | 0.198% | 506 |
| Finnishnot grpmax-eligible | 0.165% | 605 |
| Admixed American | 0.148% | 678 |
| African / African-American | 0.0986% | 1,014 |
| South Asian | 0.0872% | 1,147 |
| Middle Eastern | 0.0167% | 6,006 |
| East Asian | 0.00463% | 21,576 |
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.Pro39=
- Coding
- c.117G>A
- MANE Select
- NM_138422
- dbSNP
- rs199915192
- Type
- single nucleotide variant
- Location
- chr19:1912164 (GRCh38)
- Gene constraint
- LOEUF 1.929 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.83
Similar variants
- ADAT3 p.Pro39Leu 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
- ADAT3 p.Leu247Val 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-pro39 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown