CRYGC p.Val86=
c.258C>T · rs761447168 · VCV1571346
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.022%, sas)
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 0.12 | GERP -2.6 |
| Overall | ||
| CADD | 1.004 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.022%
South Asian · 20/91,090 alleles
Filtering AF
0.0145%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0121%
Overall
0.00136%
22/1,614,100 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.022% | 4,555 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,482 |
| European (non-Finnish) | 8.47e-05% | 1,180,057 |
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.Val86=
- Coding
- c.258C>T
- MANE Select
- NM_020989
- dbSNP
- rs761447168
- Type
- single nucleotide variant
- Location
- chr2:208128470 (GRCh38)
- Gene constraint
- LOEUF 0.941 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 96.66 · 1 PDB
- Residue 86
- the 'connecting peptide' region
Similar variants
- CRYGC p.Val86Phe Likely benign ★★ same residue
- 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
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-val86 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown