CRYGC p.Ser40=
c.120C>T · rs184571576 · VCV772583
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.66%, eas)
Conditions
1
Nuclear pulverulent cataract
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 0.23 | GERP -2.6, phastCons 0.85 |
| Overall | ||
| CADD | 9.993 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.66%
East Asian · 743/44,880 alleles
Filtering AF
1.56%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.52%
Overall
0.0518%
836/1,614,200 alleles · low-frequency
exomes 757/1,461,892 · genomes 79/152,308 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.66% | 60 |
| Remaining individualsnot grpmax-eligible | 0.0752% | 1,330 |
| South Asian | 0.0406% | 2,462 |
| Admixed American | 0.005% | 20,007 |
| African / African-American | 0.00267% | 37,522 |
| European (non-Finnish) | 0.000339% | 295,010 |
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
- Protein
- p.Ser40=
- Coding
- c.120C>T
- MANE Select
- NM_020989
- dbSNP
- rs184571576
- Type
- single nucleotide variant
- Location
- chr2:208129573 (GRCh38)
- Gene constraint
- LOEUF 0.941 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 96.66 · 1 PDB
- Residue 40
- the beta/gamma crystallin 'greek key' 1 domain; a β-strand
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-p-ser40 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown