ADAT3 p.Pro86=
c.258C>T · rs540777845 · VCV732251
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.389%, 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 -20 | GERP -2.7 |
| Overall | ||
| CADD | 0.102 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.389%
East Asian · 160/41,146 alleles
Filtering AF
0.34%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.321%
Overall
0.0108%
168/1,560,738 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.389% | 257 |
| Admixed American | 0.00562% | 17,798 |
| African / African-American | 0.00139% | 72,124 |
| European (non-Finnish) | 0.000345% | 289,873 |
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.Pro86=
- Coding
- c.258C>T
- MANE Select
- NM_138422
- dbSNP
- rs540777845
- Type
- single nucleotide variant
- Location
- chr19:1912305 (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-pro86 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown