CRYM p.Pro45=
c.135C>A · rs1180636969 · VCV439560
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00489%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>C here scores Δ0.49 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -12 | GERP -3.3 |
| Overall | ||
| CADD | 3.925 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00489%
East Asian · 2/40,898 alleles
Filtering AF
0.00081%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000303%
Overall
0.000129%
2/1,548,650 alleles · very rare
exomes 2/1,396,436 · genomes 0/152,214 · joint denominator
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
- CRYM
- Protein
- p.Pro45=
- Coding
- c.135C>A
- MANE Select
- NM_001376256
- dbSNP
- rs1180636969
- Type
- single nucleotide variant
- Location
- chr16:21278117 (GRCh38)
- Gene constraint
- LOEUF 0.841 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.06 · 1 PDB
- Residue 45
- an α-helix
Similar variants
- CRYM p.Ala178Glu Uncertain significance ★★ ⚠ same type
- CRYM p.Glu172Gly Uncertain significance ★★ ⚠ same type
- CRYM p.Leu72Val Uncertain significance ★★ ⚠ same type
- CRYM p.Met295Ile Uncertain significance ★★ ⚠ same type
- CRYM p.Thr95Ser Uncertain significance ★★ ⚠ same type
- CRYM p.Val4Leu Uncertain significance ★★ ⚠ same type
- CRYM c.171-118C>T Benign ★★ same type
- CRYM c.171-19G>A Likely benign ★★ 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/crym-p-pro45 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown