HARS1 p.Phe320=
c.960T>C · rs1581504646 · VCV764750
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0022%, 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 -1.3 | GERP -3.2 |
| Overall | ||
| CADD | 1.412 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0022%
South Asian · 2/91,074 alleles
Filtering AF
0.000365%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000137%
Overall
0.000124%
2/1,613,534 alleles · very rare
exomes 2/1,461,160 · genomes 0/152,374 · 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
- HARS1
- Protein
- p.Phe320=
- Coding
- c.960T>C
- MANE Select
- NM_002109
- dbSNP
- rs1581504646
- Type
- single nucleotide variant
- Location
- chr5:140676888 (GRCh38)
- Gene constraint
- LOEUF 0.957 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.06 · 10 PDB
- Residue 320
- a β-strand
Similar variants
- HARS1 p.Thr132Ile Pathogenic/Likely pathogenic ★★ same type
- HARS1 c.1195-1G>A Uncertain significance ★★ same type
- HARS1 c.1311+4T>C Uncertain significance ★★ same type
- HARS1 c.1312-1G>A Uncertain significance ★★ same type
- HARS1 c.631-3C>A Uncertain significance ★★ same type
- HARS1 c.90+4A>C Uncertain significance ★★ same type
- HARS1 c.952-3C>A Uncertain significance ★★ same type
- HARS1 p.Ala2Thr 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/hars1-p-phe320 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown