CRAT p.Pro568=
c.1704C>T · rs145730542 · VCV2070494
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00666%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.089 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.33 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP -7.7 | GERP -3.4 |
| Overall | ||
| CADD | 3.111 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00666%
African / African-American · 5/75,050 alleles
Filtering AF
0.00255%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00161%
Overall
0.00192%
31/1,613,268 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00666% | 15,010 |
| South Asian | 0.0022% | 45,537 |
| European (non-Finnish) | 0.00203% | 49,166 |
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.Pro568=
- Coding
- c.1704C>T
- MANE Select
- NM_000755
- dbSNP
- rs145730542
- Type
- single nucleotide variant
- Location
- chr9:129095574 (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-pro568 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown