GARS1 p.Ala100=
c.300C>G · rs781432743 · VCV1680887
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00267%, afr)
Conditions
1
Charcot-Marie-Tooth disease type 2
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 0.64 | GERP 0.51, phastCons 1 |
| Overall | ||
| CADD | 13.22 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00267%
African / African-American · 2/74,906 alleles
Filtering AF
0.000443%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000166%
Overall
0.000434%
7/1,613,938 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00267% | 37,453 |
| European (non-Finnish) | 0.000424% | 235,995 |
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
- GARS1
- Protein
- p.Ala100=
- Coding
- c.300C>G
- MANE Select
- NM_002047
- dbSNP
- rs781432743
- Type
- single nucleotide variant
- Location
- chr7:30598873 (GRCh38)
- Gene constraint
- LOEUF 0.648 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.61 · 14 PDB
- Residue 100
- the whep-trs domain; an α-helix
Similar variants
- GARS1 p.Ala100Thr Uncertain significance ★ ⚠ same residue
- GARS1 p.Asp200Asn Pathogenic/Likely pathogenic ★★ same condition
- GARS1 p.Gly294Arg Pathogenic/Likely pathogenic ★★ same condition
- GARS1 p.Gly339Arg Pathogenic/Likely pathogenic ★★ same condition
- GARS1 p.His472Arg Pathogenic ★★ same condition
- GARS1 p.Ile334Asn Pathogenic/Likely pathogenic ★★ same condition
- GARS1 p.Ile334Phe Pathogenic ★★ same condition
- GARS1 p.Ile334Thr Pathogenic/Likely pathogenic ★★ same condition
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/gars1-p-ala100 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown