ADAT3 p.Pro35Arg
c.104C>G · VCV3899407
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00562%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.027 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.16 | GERP -2.6 |
| Regional constraint | o/e 1.29 | unconstrained · MANE · 1,100 bp · p 7.8e-12 · regional, not allelic |
| Overall | ||
| CADD | 1.365 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00562%
Admixed American · 3/53,368 alleles
Filtering AF
0.00149%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000813%
Overall
0.000849%
12/1,414,126 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00562% | 17,789 |
| Remaining individualsnot grpmax-eligible | 0.00164% | 60,970 |
| European (non-Finnish) | 0.000689% | 145,162 |
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.Pro35Arg
- Coding
- c.104C>G
- MANE Select
- NM_138422
- Type
- single nucleotide variant
- Location
- chr19:1912151 (GRCh38)
- Gene constraint
- LOEUF 1.929 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.83
Similar variants
- 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
- ADAT3 p.Pro292Leu 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-pro35arg (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown