CRYGS

crystallin gamma S, the group of Beta-gamma crystallins

Basic information

Region (hg38): 3:186538441-186546702

Previous symbols: [ "CRYG8" ]

Links

ENSG00000213139 ∙ NCBI:1427 ∙ OMIM:123730 ∙ HGNC:2417 ∙ Uniprot:P22914 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• cataract 20 multiple types (Strong), mode of inheritance: AD
• early-onset sutural cataract (Supportive), mode of inheritance: AD
• early-onset lamellar cataract (Supportive), mode of inheritance: AD
• cataract 20 multiple types (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cataract 20, 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	16141006; 18587492; 19262743

ClinVar

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

• Cataract 20 multiple types (2 variants)
• Retinitis pigmentosa (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CRYGS 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				1	1	2
missense	2	2	23	1		28
nonsense			2			2
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1		1	2
non coding				4	3	7
Total	2	2	25	6	4

Variants in CRYGS

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

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

Position	Type	Phenotype	Significance	ClinVar
3-186538712-C-T		Inborn genetic diseases	Uncertain significance (Feb 23, 2023)
3-186538713-G-A		Inborn genetic diseases	Uncertain significance (Mar 08, 2024)
3-186538731-G-A		Cataract 20 multiple types	Uncertain significance (Aug 11, 2023)
3-186538783-G-T		Cataract 20 multiple types	Uncertain significance (Oct 29, 2023)
3-186538797-G-A		Cataract 20 multiple types	Uncertain significance (Dec 27, 2022)
3-186538812-C-A		Cataract 20 multiple types	Uncertain significance (May 06, 2021)
3-186538847-G-A		Inborn genetic diseases	Uncertain significance (Jan 08, 2024)
3-186538859-C-T		CRYGS-related disorder	Uncertain significance (Aug 18, 2023)
3-186538878-T-G		Inborn genetic diseases	Uncertain significance (May 01, 2023)
3-186538881-T-C		Inborn genetic diseases	Uncertain significance (Apr 07, 2023)
3-186538897-G-A		CRYGS-related disorder	Likely benign (Aug 13, 2019)
3-186538927-C-T		Cataract 20 multiple types	Benign/Likely benign (Jan 22, 2024)
3-186538928-C-T		Cataract 20 multiple types	Likely benign (Oct 29, 2023)
3-186538934-T-G		Cataract 20 multiple types • Inborn genetic diseases	Uncertain significance (May 31, 2023)
3-186538939-G-T		Cataract 20 multiple types	Benign (Dec 07, 2023)
3-186538964-C-G		Cataract 20 multiple types	Uncertain significance (Dec 02, 2024)
3-186538980-C-T		Cataract 20 multiple types	Likely benign (Oct 08, 2021)
3-186539091-C-T			Benign (Oct 01, 2018)
3-186539172-C-T			Likely benign (Oct 09, 2018)
3-186539251-C-T			Likely benign (Mar 26, 2020)
3-186539366-C-T		Cataract 20 multiple types	Uncertain significance (Sep 29, 2016)
3-186539371-C-T		Cataract 20 multiple types	Uncertain significance (Mar 21, 2021)
3-186539372-A-G		Cataract 20 multiple types	Uncertain significance (Jan 15, 2020)
3-186539383-C-T		Cataract 20 multiple types	Uncertain significance (Oct 17, 2022)
3-186539387-C-T		CRYGS-related disorder	Uncertain significance (Apr 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CRYGS	protein_coding	protein_coding	ENST00000392499	3	8262

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0230	0.919	125725	0	22	125747	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.243	102	109	0.935	0.00000657	1181
Missense in Polyphen		23	33.592	0.68468		423
Synonymous	1.11	27	35.4	0.763	0.00000188	313
Loss of Function	1.62	4	9.33	0.429	4.83e-7	104

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000333	0.000333
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000969	0.0000967
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Crystallins are the dominant structural components of the vertebrate eye lens.
• Disease: DISEASE: Cataract 20, multiple types (CTRCT20) [MIM:116100]: 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. CTRCT20 includes progressive polymorphic anterior, posterior, or peripheral cortical. {ECO:0000269|PubMed:16141006}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Intolerance Scores

• loftool: 0.560
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.42

Haploinsufficiency Scores

• pHI: 0.116
• hipred: N
• hipred_score: 0.380
• ghis: 0.613

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.192

Gene Damage Prediction

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

Mouse Genome Informatics

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

Gene ontology

• Biological process: morphogenesis of an epithelium;lens development in camera-type eye
• Molecular function: structural constituent of eye lens;protein binding