CRAT p.Glu366=
c.1098G>A · rs141081974 · VCV810439
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.95%, 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 -0.005 | GERP -3.4, phastCons 0.78 |
| Overall | ||
| CADD | 1.156 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.95%
South Asian · 1,749/89,496 alleles
Filtering AF
1.88%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.85%
Overall
0.242%
3,875/1,603,194 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.95% | 51 |
| Middle Eastern | 1.05% | 95 |
| Ashkenazi Jewishnot grpmax-eligible | 0.922% | 108 |
| Remaining individualsnot grpmax-eligible | 0.337% | 296 |
| Finnishnot grpmax-eligible | 0.306% | 327 |
| Admixed American | 0.128% | 778 |
| European (non-Finnish) | 0.111% | 903 |
| African / African-American | 0.0203% | 4,926 |
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.Glu366=
- Coding
- c.1098G>A
- MANE Select
- NM_000755
- dbSNP
- rs141081974
- Type
- single nucleotide variant
- Location
- chr9:129098638 (GRCh38)
- Gene constraint
- LOEUF 1.111 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.75 · 3 PDB
Similar variants
- CRAT p.Glu366Gly Uncertain significance ★ ⚠ same residue
- CRAT p.Glu366Lys Uncertain significance ★ ⚠ 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-glu366 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown