CRYGC

crystallin gamma C, the group of Beta-gamma crystallins

Basic information

Region (hg38): 2:208128136-208129828

Previous symbols: [ "CRYG3" ]

Links

ENSG00000163254 ∙ NCBI:1420 ∙ OMIM:123680 ∙ HGNC:2410 ∙ Uniprot:P07315 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• cataract 9 multiple types (Definitive), mode of inheritance: AD
• cataract 2, multiple types (Strong), mode of inheritance: AD
• cataract - microcornea syndrome (Supportive), mode of inheritance: AD
• pulverulent cataract (Supportive), mode of inheritance: AD
• early-onset nuclear cataract (Supportive), mode of inheritance: AD
• early-onset lamellar cataract (Supportive), mode of inheritance: AD
• cataract 2, multiple types (Definitive), mode of inheritance: AD
• cataract 2, multiple types (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cataract 2, multiple types	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Ophthalmologic	8190472; 10521291; 10914683; 12011157; 18587492; 18618005; 19204787; 22052681; 22876111

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CRYGC gene.

• Nuclear pulverulent cataract (35 variants)
• not provided (18 variants)
• Inborn genetic diseases (11 variants)
• Cataract 2, multiple types (6 variants)
• not specified (1 variants)
• CRYGC-related condition (1 variants)
• Usher syndrome type 2C (1 variants)
• Cataract 2, Coppock-like (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CRYGC gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				3	4	7
missense	1	1	25	4	2	33
nonsense	3	1	1			5
start loss						0
frameshift	5	1				6
inframe indel			1			1
splice donor/acceptor (+/-2bp)			1			1
splice region				1		1
non coding				4	4	8
Total	9	3	28	11	10

Variants in CRYGC

This is a list of pathogenic ClinVar variants found in the CRYGC region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-208128194-T-G		CRYGC-related disorder	Likely benign (Apr 09, 2019)
2-208128226-G-A		Cataract 2, multiple types • Nuclear pulverulent cataract	Conflicting classifications of pathogenicity (Nov 27, 2023)
2-208128231-G-A		Cataract 2, multiple types • Developmental cataract	Pathogenic (Jan 09, 2015)
2-208128237-G-A		Inborn genetic diseases	Uncertain significance (Oct 05, 2022)
2-208128249-A-G		Inborn genetic diseases	Uncertain significance (Dec 22, 2023)
2-208128252-G-GC		Nuclear pulverulent cataract • CRYGC-related disorder	Conflicting classifications of pathogenicity (Oct 30, 2023)
2-208128257-C-T		Cataract 2, multiple types	Pathogenic (Jan 01, 2012)
2-208128258-C-T		Cataract 2, multiple types	Pathogenic (May 09, 2024)
2-208128259-A-CT			Pathogenic (Dec 01, 2018)
2-208128270-C-T		Inborn genetic diseases	Uncertain significance (Nov 17, 2022)
2-208128278-C-A		Nuclear pulverulent cataract • Inborn genetic diseases	Uncertain significance (Sep 12, 2022)
2-208128296-G-C			Pathogenic (Jun 20, 2018)
2-208128296-G-T		CRYGC-related disorder	Likely pathogenic (Feb 27, 2024)
2-208128301-G-A			Pathogenic (Mar 29, 2016)
2-208128303-CG-C			Pathogenic (Oct 07, 2019)
2-208128304-G-C			Likely pathogenic (Oct 07, 2019)
2-208128304-GC-G		Cataract 2, multiple types	Pathogenic (Feb 09, 2018)
2-208128304-G-GC		Nuclear pulverulent cataract	Pathogenic (Mar 19, 2019)
2-208128309-C-CG		Nuclear pulverulent cataract	Likely pathogenic (Nov 12, 2021)
2-208128311-GTAGTTG-TCTACGAGGGTATTGCCCCGTCTACGAGGTATTGCCCGTCTACGAGGGTATTGCCCCGTCTACGA		Nuclear pulverulent cataract	Likely pathogenic (Nov 28, 2022)
2-208128315-T-C		Nuclear pulverulent cataract	Uncertain significance (Jul 29, 2023)
2-208128325-C-A			Likely pathogenic (-)
2-208128325-C-T		Cataract 2, multiple types	Uncertain significance (Jul 07, 2022)
2-208128326-G-C		Nuclear pulverulent cataract	Conflicting classifications of pathogenicity (May 29, 2022)
2-208128333-AC-A		Cataract 2, multiple types	Pathogenic (Feb 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CRYGC	protein_coding	protein_coding	ENST00000282141	3	1694

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000606	0.739	125624	0	124	125748	0.000493

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.604	127	109	1.16	0.00000779	1139
Missense in Polyphen		24	30.291	0.79232		351
Synonymous	-0.628	48	42.8	1.12	0.00000269	326
Loss of Function	0.929	6	9.01	0.666	4.77e-7	87

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000122	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00448	0.00449
European (Non-Finnish)	0.000176	0.000176
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Crystallins are the dominant structural components of the vertebrate eye lens.
• Disease: DISEASE: Cataract 2, multiple types (CTRCT2) [MIM:604307]: An opacification of the crystalline lens of the eye that frequently results in visual impairment or blindness. Opacities vary in morphology, are often confined to a portion of the lens, and may be static or progressive. CTRCT2 includes Coppock-like cataract, among others. Coppock-like cataract is a congenital pulverulent disk-like opacity involving the embryonic nucleus with many tiny white dots in the lamellar portion of the lens. It is usually bilateral and dominantly inherited. In some cases, CTRCT2 is associated with microcornea without any other systemic anomaly or dysmorphism. Microcornea is defined by a corneal diameter inferior to 10 mm in both meridians in an otherwise normal eye. {ECO:0000269|PubMed:10521291, ECO:0000269|PubMed:10914683, ECO:0000269|PubMed:12011157, ECO:0000269|PubMed:12601044, ECO:0000269|PubMed:18587492, ECO:0000269|PubMed:22052681, ECO:0000269|PubMed:22876111}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.396

Intolerance Scores

• loftool: 0.465
• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.27

Haploinsufficiency Scores

• pHI: 0.118
• hipred: N
• hipred_score: 0.245
• ghis: 0.443

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.578

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Crygc
• Phenotype: vision/eye phenotype

Gene ontology

• Biological process: visual perception
• Cellular component: nucleus;cytoplasm
• Molecular function: structural constituent of eye lens;protein binding