CRYGB

crystallin gamma B, the group of Beta-gamma crystallins

Basic information

Region (hg38): 2:208142573-208146158

Previous symbols: [ "CRYG2" ]

Links

ENSG00000182187 ∙ NCBI:1419 ∙ OMIM:123670 ∙ HGNC:2409 ∙ Uniprot:P07316 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• early-onset anterior polar cataract (Supportive), mode of inheritance: AD
• total early-onset cataract (Supportive), mode of inheritance: AD
• early-onset lamellar cataract (Supportive), mode of inheritance: AD
• cataract 39 multiple types (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cataract 39, 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	23288985

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CRYGB 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	3	6
missense			15	2	2	19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				3	11	14
Total	0	0	15	8	16

Variants in CRYGB

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

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

Position	Type	Phenotype	Significance	ClinVar
2-208142628-C-T		CRYGB-related disorder	Likely benign (May 09, 2019)
2-208142653-G-A		Cataract 39 multiple types	Benign (Dec 20, 2018)
2-208142657-C-T		not specified	Uncertain significance (Dec 21, 2022)
2-208142680-A-T		not specified	Uncertain significance (May 29, 2024)
2-208142688-C-G		Cataract 39 multiple types • not specified	Uncertain significance (Aug 09, 2022)
2-208142712-A-T		not specified	Uncertain significance (Jan 03, 2024)
2-208142738-C-T		Cataract 39 multiple types	Uncertain significance (Mar 10, 2022)
2-208142793-G-C		not specified	Uncertain significance (Dec 03, 2024)
2-208142835-T-G		Cataract 39 multiple types	Benign (Jan 27, 2024)
2-208142842-G-A		CRYGB-related disorder	Likely benign (Sep 11, 2024)
2-208142854-T-C		Cataract 39 multiple types • CRYGB-related disorder	Benign (Mar 27, 2023)
2-208142864-C-A		Cataract 39 multiple types	Uncertain significance (Jun 15, 2023)
2-208142876-T-C		not specified	Uncertain significance (Jan 24, 2023)
2-208142883-C-T		not specified	Uncertain significance (Nov 15, 2024)
2-208142894-A-G		not specified	Uncertain significance (Dec 10, 2024)
2-208142907-C-T		not specified	Uncertain significance (Jun 16, 2024)
2-208143062-A-G			Benign (Jun 29, 2018)
2-208143069-A-G			Benign (Jul 21, 2018)
2-208145506-T-C			Benign (Jul 21, 2018)
2-208145545-T-C			Benign (Jun 29, 2018)
2-208145688-CA-C			Benign (Aug 24, 2019)
2-208145688-CAA-C			Likely benign (Aug 26, 2019)
2-208145688-C-CA			Benign (Aug 31, 2019)
2-208145775-G-A		Cataract 39 multiple types	Uncertain significance (Jan 16, 2022)
2-208145782-T-C		Cataract 39 multiple types • not specified	Uncertain significance (May 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CRYGB	protein_coding	protein_coding	ENST00000260988	3	3596

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.14e-8	0.0888	125714	0	33	125747	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.454	120	107	1.12	0.00000625	1156
Missense in Polyphen		33	29.428	1.1214		351
Synonymous	-0.529	44	39.8	1.11	0.00000238	313
Loss of Function	-0.487	10	8.47	1.18	3.61e-7	94

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000517	0.000514
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000882	0.0000879
Middle Eastern	0.000163	0.000163
South Asian	0.000255	0.000229
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Crystallins are the dominant structural components of the vertebrate eye lens.
• Disease: DISEASE: Cataract 39, multiple types (CTRCT39) [MIM:615188]: 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. In general, the more posteriorly located and dense an opacity, the greater the impact on visual function. CTRCT39 includes lamellar, anterior polar, and complete cataracts. {ECO:0000269|PubMed:23288985}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.703
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63

Haploinsufficiency Scores

• pHI: 0.150
• hipred: N
• hipred_score: 0.170
• ghis: 0.435

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.135

Gene Damage Prediction

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

Mouse Genome Informatics

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

Gene ontology

• Biological process: visual perception;lens fiber cell morphogenesis
• Cellular component: cellular_component;nucleus;cytoplasm
• Molecular function: structural constituent of eye lens