CRYGA

crystallin gamma A, the group of Beta-gamma crystallins

Basic information

Region (hg38): 2:208160740-208163589

Previous symbols: [ "CRYG1" ]

Links

ENSG00000168582 ∙ NCBI:1418 ∙ OMIM:123660 ∙ HGNC:2408 ∙ Uniprot:P11844 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CRYGA 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						0
missense			28	2		30
nonsense					1	1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	2	1

Variants in CRYGA

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

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

Position	Type	Phenotype	Significance	ClinVar
2-208160815-C-T		not specified	Uncertain significance (Feb 07, 2023)
2-208160823-C-T		not specified	Uncertain significance (Mar 07, 2024)
2-208160824-G-A		not specified	Uncertain significance (Sep 11, 2024)
2-208160848-C-T		not specified	Uncertain significance (Jan 18, 2023)
2-208160858-C-A		See cases	Uncertain significance (Aug 28, 2023)
2-208160870-C-A		not specified	Uncertain significance (Oct 30, 2023)
2-208160881-C-T		not specified	Uncertain significance (Jun 25, 2024)
2-208160884-C-T		not specified	Uncertain significance (Apr 09, 2024)
2-208160904-C-T		not specified	Uncertain significance (May 28, 2024)
2-208160910-C-A		not specified	Uncertain significance (Jun 24, 2022)
2-208160910-C-T		not specified	Uncertain significance (Nov 21, 2023)
2-208160928-T-A		not specified	Uncertain significance (Feb 10, 2022)
2-208160928-T-C		not specified	Uncertain significance (Dec 11, 2023)
2-208160937-C-A		not specified	Uncertain significance (Dec 03, 2024)
2-208160940-C-T		CRYGA-related disorder	Likely benign (May 27, 2022)
2-208160947-C-G		not specified	Uncertain significance (Aug 17, 2021)
2-208160972-A-T		CRYGA-related disorder	Benign (May 28, 2019)
2-208161001-C-T		not specified	Uncertain significance (Mar 23, 2022)
2-208161016-G-C		not specified	Uncertain significance (Dec 08, 2023)
2-208161033-C-T		not specified	Uncertain significance (Apr 19, 2024)
2-208161034-G-A		CRYGA-related disorder	Benign (Dec 31, 2019)
2-208161040-C-T		not specified	Uncertain significance (Oct 07, 2024)
2-208161072-C-G		not specified	Uncertain significance (Oct 12, 2024)
2-208161072-C-T		not specified	Uncertain significance (Jan 19, 2024)
2-208163208-G-C		not specified	Uncertain significance (Mar 08, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CRYGA	protein_coding	protein_coding	ENST00000304502	3	2837

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.33e-10	0.0298	124900	16	830	125746	0.00337

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.651	136	116	1.17	0.00000782	1134
Missense in Polyphen		49	35.988	1.3615		386
Synonymous	-0.326	49	46.2	1.06	0.00000306	329
Loss of Function	-0.677	13	10.6	1.22	7.10e-7	92

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0238	0.0238
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000326
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000176	0.000176
Middle Eastern	0.000326	0.000326
South Asian	0.000131	0.000131
Other	0.00326	0.00326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Crystallins are the dominant structural components of the vertebrate eye lens.

Recessive Scores

• pRec: 0.137

Intolerance Scores

• loftool: 0.692
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.22

Haploinsufficiency Scores

• pHI: 0.168
• hipred: N
• hipred_score: 0.285
• ghis: 0.445

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

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

Gene ontology

• Biological process: lens development in camera-type eye;visual perception
• Cellular component: cellular_component
• Molecular function: structural constituent of eye lens