YARS2 p.Phe220=
c.660T>C · rs769135460 · VCV2129744
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00549%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -4.3 | |
| Overall | ||
| CADD | 6.58 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00549%
South Asian · 5/91,082 alleles
Filtering AF
0.0021%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00136%
Overall
0.00031%
5/1,614,166 alleles · very rare
exomes 5/1,461,886 · genomes 0/152,280 · 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.Phe220=
- Coding
- c.660T>C
- MANE Select
- NM_001040436
- dbSNP
- rs769135460
- Type
- single nucleotide variant
- Location
- chr12:32755215 (GRCh38)
- Gene constraint
- LOEUF 1.035 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.57 · 2 PDB
- Residue 220
- an α-helix
Similar variants
- YARS2 p.Phe220Leu 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-phe220 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown