ADAT3 p.Ser49=
c.147C>T · rs138302527 · VCV3025735
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00453%, 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 -12 | GERP -3.1 |
| Overall | ||
| CADD | 0.022 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00453%
European (non-Finnish) · 53/1,169,910 alleles
Filtering AF
0.00353%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0032%
Overall
0.00359%
57/1,585,876 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00453% | 22,074 |
| Remaining individualsnot grpmax-eligible | 0.00325% | 30,747 |
| Admixed American | 0.00178% | 56,286 |
| African / African-American | 0.00134% | 74,452 |
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.Ser49=
- Coding
- c.147C>T
- MANE Select
- NM_138422
- dbSNP
- rs138302527
- Type
- single nucleotide variant
- Location
- chr19:1912194 (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-ser49 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown