CRAT p.Ala346=
c.1038G>A · rs771615619 · VCV2960057
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00439%, 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 -14 | GERP -3.8 |
| Overall | ||
| CADD | 0.095 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00439%
South Asian · 4/91,070 alleles
Filtering AF
0.00143%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000891%
Overall
0.00112%
18/1,613,606 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00439% | 22,767 |
| East Asian | 0.00223% | 44,888 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,476 |
| European (non-Finnish) | 0.00102% | 98,330 |
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
- CRAT
- Protein
- p.Ala346=
- Coding
- c.1038G>A
- MANE Select
- NM_000755
- dbSNP
- rs771615619
- Type
- single nucleotide variant
- Location
- chr9:129099913 (GRCh38)
- Gene constraint
- LOEUF 1.111 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.75 · 3 PDB
Similar variants
- CRAT p.Ala346Val Uncertain significance ★ ⚠ same residue
- CRAT p.Ala346Thr Likely benign ★ ⚠ same residue
- CRAT p.Ala260Pro Uncertain significance ★★ ⚠ same type
- CRAT p.Ala262Thr Uncertain significance ★★ ⚠ same type
- CRAT p.Ala544Thr Uncertain significance ★★ ⚠ same type
- CRAT p.Ala546Thr Uncertain significance ★★ ⚠ same type
- CRAT p.Ala596Thr Uncertain significance ★★ ⚠ same type
- CRAT p.Ala596Val 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/crat-p-ala346 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown