CRYGC p.Ser119=
c.357C>T · rs61736036 · VCV465774
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.4%, afr)
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 -0.46 | GERP -5 |
| Overall | ||
| CADD | 5.711 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.4%
African / African-American · 3,302/75,018 alleles
Filtering AF
4.28%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.23%
Overall
0.242%
3,904/1,614,150 alleles · low-frequency
exomes 1,990/1,461,892 · genomes 1,914/152,258 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.4% | 23 |
| Middle Eastern | 0.446% | 224 |
| Remaining individualsnot grpmax-eligible | 0.381% | 263 |
| Admixed American | 0.298% | 335 |
| Finnishnot grpmax-eligible | 0.025% | 4,002 |
| South Asian | 0.0165% | 6,072 |
| European (non-Finnish) | 0.0108% | 9,292 |
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.Ser119=
- Coding
- c.357C>T
- MANE Select
- NM_020989
- dbSNP
- rs61736036
- Type
- single nucleotide variant
- Location
- chr2:208128371 (GRCh38)
- Gene constraint
- LOEUF 0.941 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 96.66 · 1 PDB
- Residue 119
- the beta/gamma crystallin 'greek key' 3 domain
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-ser119 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown