YARS2 p.Pro340=
c.1020A>G · rs1049274174 · VCV1968374
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.004%, afr)
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 -2.5 | |
| Overall | ||
| CADD | 7.453 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.004%
African / African-American · 3/74,934 alleles
Filtering AF
0.00106%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000495%
Overall
0.000186%
3/1,614,078 alleles · very rare
exomes 1/1,461,880 · genomes 2/152,198 · joint denominator
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
- YARS2
- Protein
- p.Pro340=
- Coding
- c.1020A>G
- MANE Select
- NM_001040436
- dbSNP
- rs1049274174
- Type
- single nucleotide variant
- Location
- chr12:32750802 (GRCh38)
- Gene constraint
- LOEUF 1.035 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.57 · 2 PDB
- Residue 340
- an α-helix
Similar variants
- YARS2 p.Pro340Ser Uncertain significance ★ ⚠ same residue
- YARS2 p.Asp311Glu Pathogenic/Likely pathogenic ★★ ⚠ same type
- YARS2 p.Glu212Ter Pathogenic/Likely pathogenic ★★ same type
- YARS2 p.Ile251Val Likely pathogenic ★★ ⚠ same type
- YARS2 p.Phe52Leu Pathogenic/Likely pathogenic ★★ ⚠ same type
- YARS2 p.Ser33Ter Pathogenic/Likely pathogenic ★★ same type
- YARS2 p.Ala139Val Uncertain significance ★★ ⚠ same type
- YARS2 p.Ala31Thr 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/yars2-p-pro340 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown