CRAT p.Ser318=
c.954C>T · rs113579980 · VCV1168217
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.453%, afr)
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 -9.4 | GERP -4 |
| Overall | ||
| CADD | 0.72 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.453%
African / African-American · 340/75,054 alleles
Filtering AF
0.413%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.398%
Overall
0.0256%
413/1,613,636 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.453% | 221 |
| Remaining individualsnot grpmax-eligible | 0.0384% | 2,604 |
| Admixed American | 0.0383% | 2,609 |
| Middle Eastern | 0.0165% | 6,052 |
| South Asian | 0.00769% | 13,010 |
| European (non-Finnish) | 0.00153% | 65,553 |
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.Ser318=
- Coding
- c.954C>T
- MANE Select
- NM_000755
- dbSNP
- rs113579980
- Type
- single nucleotide variant
- Location
- chr9:129100541 (GRCh38)
- Gene constraint
- LOEUF 1.111 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.75 · 3 PDB
- Residue 318
- a turn
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-ser318 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown