TARS2 p.Pro319=
c.957T>C · VCV4909864
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0231%, sas)
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 -7 | GERP -3.3 |
| Overall | ||
| CADD | 2.255 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0231%
South Asian · 21/91,078 alleles
Filtering AF
0.0154%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0129%
Overall
0.00157%
23/1,461,854 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0231% | 4,337 |
| European (non-Finnish) | 0.000169% | 589,998 |
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
- TARS2
- Protein
- p.Pro319=
- Coding
- c.957T>C
- MANE Select
- NM_025150
- Type
- single nucleotide variant
- Location
- chr1:150496845 (GRCh38)
- Gene constraint
- LOEUF 0.76 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.19
Similar variants
- TARS2 p.Pro319Leu Uncertain significance ★ ⚠ same residue
- TARS2 c.695+3A>G Pathogenic/Likely pathogenic ★★ same type
- TARS2 p.Ala149Thr Uncertain significance ★★ ⚠ same type
- TARS2 p.Ala17Thr Uncertain significance ★★ ⚠ same type
- TARS2 p.Arg246Trp Uncertain significance ★★ ⚠ same type
- TARS2 p.Arg346Cys Uncertain significance ★★ ⚠ same type
- TARS2 p.Arg438Gly Uncertain significance ★★ ⚠ same type
- TARS2 p.Arg480His 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/tars2-p-pro319 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown