CRYGC c.252+14A>G
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.103%, eas)
Conditions
1
Nuclear pulverulent cataract
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +14 | near-intronic (+14 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.4 | GERP -4.3 |
| Non-coding constraint | Z 0.46 | 1 kb window · o/e 0.97 · regional · uncalibrated |
| Overall | ||
| CADD | 0.15 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.103%
East Asian · 46/44,870 alleles
Filtering AF
0.0789%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0706%
Overall
0.00315%
46/1,459,648 alleles · rare
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
- CRYGC
- Coding
- c.252+14A>G
- MANE Select
- NM_020989
- Type
- single nucleotide variant
- Location
- chr2:208129427 (GRCh38)
- Gene constraint
- LOEUF 0.941 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 96.66 · 1 PDB
Similar variants
- CRYGC p.Arg122His Uncertain significance ★★ ⚠ same condition
- CRYGC p.Arg15His Uncertain significance ★★ ⚠ same condition
- CRYGC p.Arg77Cys Uncertain significance ★★ ⚠ same condition
- CRYGC p.Glu150Asp Uncertain significance ★★ ⚠ same condition
- CRYGC p.Pro49Thr Uncertain significance ★★ ⚠ same condition
- CRYGC c.10-10T>C Benign/Likely benign ★★ same condition
- CRYGC p.Gly41= Benign ★★ same condition
- CRYGC p.Pro28= Benign/Likely 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/crygc-c-252-plus-14a-g (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown