CRYM p.Val289=
c.867G>C · VCV4707688
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000509%, nfe)
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 -0.19 | GERP 0.056, phastCons 0.26 |
| Overall | ||
| CADD | 7.668 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000509%
European (non-Finnish) · 6/1,179,662 alleles
Filtering AF
0.000183%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00012%
Overall
0.000372%
6/1,613,554 alleles · very rare
exomes 5/1,461,444 · genomes 1/152,110 · 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.Val289=
- Coding
- c.867G>C
- MANE Select
- NM_001376256
- Type
- single nucleotide variant
- Location
- chr16:21261267 (GRCh38)
- Gene constraint
- LOEUF 0.841 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.06 · 1 PDB
- Residue 289
- a β-strand
Similar variants
- CRYM p.Val289Met Uncertain significance ★ ⚠ same residue
- 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
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-val289 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown