CRYGD p.Tyr63=
c.189T>C · rs200911604 · VCV260060
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.212%, eas)
Conditions
1
cataract 4 multiple types
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 3.8 | GERP 0.61, phastCons 1 |
| Overall | ||
| CADD | 6.265 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.212%
East Asian · 95/44,872 alleles
Filtering AF
0.177%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.164%
Overall
0.00633%
102/1,611,656 alleles · rare
exomes 92/1,459,354 · genomes 10/152,302 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.212% | 472 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,332 |
| South Asian | 0.0011% | 90,996 |
| European (non-Finnish) | 0.000424% | 235,977 |
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
- CRYGD
- Protein
- p.Tyr63=
- Coding
- c.189T>C
- MANE Select
- NM_006891
- dbSNP
- rs200911604
- Type
- single nucleotide variant
- Location
- chr2:208124175 (GRCh38)
- Gene constraint
- LOEUF 1.796 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.45 · 16 PDB
- Residue 63
- a UniProt-annotated variant site (in ctrct4; uncertain significance); the beta/gamma crystallin 'greek key' 2 domain; a β-strand
Similar variants
- CRYGD p.Tyr63His Uncertain significance ★ ⚠ same residue
- CRYGD p.Arg140Ter Pathogenic ★★ same condition
- CRYGD p.Arg15Cys Pathogenic ★★ ⚠ same condition
- CRYGD p.Pro24Thr Pathogenic/Likely pathogenic ★★ ⚠ same condition
- CRYGD p.Asn161Ser Uncertain significance ★★ ⚠ same condition
- CRYGD c.10-7C>G Benign ★★ same condition
- CRYGD c.252+10T>A Benign/Likely benign ★★ same condition
- CRYGD c.252+7A>G Benign ★★ same condition
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/crygd-p-tyr63 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown