CRYGA p.Pro119=
c.357T>A · rs116555712 · VCV3038636
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.06%, afr)
Conditions
1
CRYGA-related disorder
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 -1.2 | GERP -1.1 |
| Overall | ||
| CADD | 5.143 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.06%
African / African-American · 795/74,946 alleles
Filtering AF
1%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.975%
Overall
0.0553%
890/1,610,812 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.06% | 94 |
| Remaining individualsnot grpmax-eligible | 0.0673% | 1,486 |
| Admixed American | 0.0633% | 1,579 |
| Middle Eastern | 0.0165% | 6,058 |
| South Asian | 0.0033% | 30,342 |
| European (non-Finnish) | 0.000935% | 107,004 |
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
- CRYGA
- Protein
- p.Pro119=
- Coding
- c.357T>A
- MANE Select
- NM_014617
- dbSNP
- rs116555712
- Type
- single nucleotide variant
- Location
- chr2:208160972 (GRCh38)
- Gene constraint
- LOEUF 1.245 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.14
- Residue 119
- the beta/gamma crystallin 'greek key' 3 domain
Disease context
CRYGA-related disorder
Similar variants
- CRYGA p.Arg80His Conflicting classifications of pathogenicity ★ ⚠ same condition
- CRYGA p.Asn18Ile Benign same condition
- CRYGA p.Cys130Tyr Likely benign same condition
- CRYGA p.Leu58= Likely benign same condition
- CRYGA p.Arg99Ter Benign ★★ same type
- CRYGA p.Ala110Thr Uncertain significance ★ ⚠ same type
- CRYGA p.Arg140Gln Uncertain significance ★ ⚠ same type
- CRYGA p.Arg140Leu Uncertain significance ★ ⚠ 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/cryga-p-pro119 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown