CRYGC p.Ala159fs
c.475dup · rs1271901479 · VCV2856619
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 3 submitters
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
ultra-rare (gnomAD MAF 6.705e-06)
Conditions
1
CRYGC-related disorders
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | escapes | premature termination codon in the last exon (3 of 3) — the truncated protein is likely expressed. PVS1 input, not an applied code |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 9.5 | GERP 2.5, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
dbSNP / gnomAD
Global frequency
0.00067%
via dbSNP · ultra-rare
No ancestry breakdown or filtering allele frequency is available for this variant, so BA1/BS1 cannot be assessed from this figure alone.
Variant & gene context
- Gene
- CRYGC
- Protein
- p.Ala159fs
- Coding
- c.475dup
- MANE Select
- NM_020989
- dbSNP
- rs1271901479
- Type
- Duplication
- Location
- chr2:208128252 (GRCh38)
- Gene constraint
- LOEUF 0.941 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 96.66 · 1 PDB
- Residue 159
- a UniProt-annotated variant site (in ctrct2; uncertain significance); the beta/gamma crystallin 'greek key' 4 domain
Disease context
CRYGC-related disorders
Similar variants
- CRYGC p.Ser78Phe Likely pathogenic ★ same condition
- CRYGC p.Gly53fs Likely pathogenic same condition
- CRYGC p.Tyr139Ter Pathogenic same condition
- CRYGC p.Tyr144Ter Likely pathogenic same condition
- CRYGC p.Arg168Gln Uncertain significance ⚠ same condition
- CRYGC c.*9A>C Likely benign same condition
- CRYGC p.Arg140fs Likely pathogenic ★ same type
- CRYGC c.7_9+1dup 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/crygc-p-ala159fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown