CRIPTO p.Gly151=
c.453C>G · rs181142338 · VCV713454
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.497%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.26 | acceptor loss, 4 bp away · masked 0 · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.54 | GERP -3.1 |
| Overall | ||
| CADD | 0.447 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.497%
East Asian · 223/44,876 alleles
Filtering AF
0.443%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.423%
Overall
0.024%
387/1,613,382 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.497% | 201 |
| Remaining individualsnot grpmax-eligible | 0.198% | 504 |
| Admixed American | 0.055% | 1,819 |
| African / African-American | 0.00133% | 75,024 |
| South Asian | 0.0011% | 91,062 |
| European (non-Finnish) | 0.000424% | 235,865 |
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
- CRIPTO
- Protein
- p.Gly151=
- Coding
- c.453C>G
- MANE Select
- NM_003212
- dbSNP
- rs181142338
- Type
- single nucleotide variant
- Location
- chr3:46581136 (GRCh38)
- Structure
- AlphaFold pLDDT 67.47
Similar variants
- CRIPTO p.Gly151Ala Uncertain significance ★ ⚠ same residue
- CRIPTO p.Gly151Asp Uncertain significance ★ ⚠ same residue
- CRIPTO c.339-8A>G Benign ★★ same type
- CRIPTO p.Arg111Gly Benign ★★ ⚠ same type
- CRIPTO p.Arg111His Uncertain significance ★ ⚠ same type
- CRIPTO p.Arg171His Uncertain significance ★ ⚠ same type
- CRIPTO p.Arg38Cys Uncertain significance ★ ⚠ same type
- CRIPTO p.Arg38His 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/cripto-p-gly151 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown