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.

• not_specified (37 variants)
• CRYGA-related_disorder (6 variants)
• not_provided (2 variants)
• Developmental_cataract (1 variants)
• See_cases (1 variants)

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. These statistics are base on transcript: NM_000014617.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	1	2
missense			37	4	1	42
nonsense					1	1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	37	5	3

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