Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 8.5%, afr) — too common for a highly-penetrant pathogenic allele
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 -3.4 | GERP -4 |
| Overall | ||
| CADD | 3.959 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.5%
African / African-American · 6,379/75,040 alleles
Filtering AF
8.33%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 8.26%
Overall
0.46%
7,422/1,613,330 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 8.5% | 12 |
| Remaining individualsnot grpmax-eligible | 0.581% | 172 |
| Admixed American | 0.538% | 186 |
| Middle Eastern | 0.314% | 318 |
| European (non-Finnish) | 0.0276% | 3,619 |
| South Asian | 0.0132% | 7,588 |
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.Phe323=
- Coding
- c.969C>T
- MANE Select
- NM_000755
- dbSNP
- rs1127926
- Type
- single nucleotide variant
- Location
- chr9:129100526 (GRCh38)
- Gene constraint
- LOEUF 1.111 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.75 · 3 PDB
Similar variants
- 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
- CRAT p.Ala600Thr Uncertain significance ★★ ⚠ same type
- CRAT p.Ala604Val 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-phe323 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown