CRYBG1

crystallin beta-gamma domain containing 1, the group of Beta-gamma crystallin domain containing

Basic information

Region (hg38): 6:106360717-106572017

Previous symbols: [ "ST4", "AIM1" ]

Links

ENSG00000112297 ∙ NCBI:202 ∙ OMIM:601797 ∙ HGNC:356 ∙ Uniprot:Q9Y4K1 ∙ 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 CRYBG1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CRYBG1 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				4		4
missense			103	5		108
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				2	4	6
Total	0	0	103	11	4

Variants in CRYBG1

This is a list of pathogenic ClinVar variants found in the CRYBG1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-106512388-C-T		not specified	Uncertain significance (Jun 29, 2023)
6-106512402-G-C		not specified	Uncertain significance (Oct 26, 2022)
6-106512468-G-A		not specified	Uncertain significance (Apr 09, 2024)
6-106512507-G-C		not specified	Uncertain significance (Jun 18, 2021)
6-106512513-A-G		not specified	Uncertain significance (Jun 06, 2023)
6-106512561-G-T		not specified	Uncertain significance (Oct 20, 2023)
6-106512592-C-A		not specified	Uncertain significance (Dec 19, 2023)
6-106512720-G-T		not specified	Uncertain significance (Sep 01, 2021)
6-106512732-G-A		not specified	Uncertain significance (Jul 17, 2023)
6-106512784-C-T		not specified	Uncertain significance (Jun 28, 2022)
6-106512814-C-T		not specified	Likely benign (Jun 11, 2024)
6-106512825-G-A		not specified	Uncertain significance (Apr 08, 2022)
6-106512832-C-T		not specified	Uncertain significance (Aug 10, 2021)
6-106512924-C-G		not specified	Uncertain significance (Sep 27, 2022)
6-106512945-G-A		not specified	Uncertain significance (Aug 10, 2023)
6-106512972-G-T		not specified	Uncertain significance (Apr 08, 2024)
6-106512996-C-A		not specified	Uncertain significance (Jan 31, 2023)
6-106519271-G-A		not specified	Uncertain significance (Feb 06, 2023)
6-106519292-A-G		not specified	Uncertain significance (Jul 12, 2022)
6-106519313-G-A		not specified	Uncertain significance (Apr 08, 2024)
6-106519337-C-T		not specified	Uncertain significance (Oct 26, 2021)
6-106519351-G-A		not specified	Uncertain significance (Apr 26, 2023)
6-106519442-A-C		not specified	Uncertain significance (May 14, 2024)
6-106519453-A-G		not specified	Likely benign (Apr 19, 2024)
6-106519475-C-T		not specified	Uncertain significance (Dec 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CRYBG1	protein_coding	protein_coding	ENST00000369066	20	58597

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.51e-33	0.00486	125199	1	548	125748	0.00219

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0567	929	924	1.01	0.0000460	11268
Missense in Polyphen		274	316.51	0.86569		4083
Synonymous	-0.908	373	351	1.06	0.0000191	3349
Loss of Function	1.50	58	71.7	0.809	0.00000397	876

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00314	0.00312
Ashkenazi Jewish	0.00263	0.00258
East Asian	0.00792	0.00786
Finnish	0.000787	0.000786
European (Non-Finnish)	0.00157	0.00152
Middle Eastern	0.00792	0.00786
South Asian	0.00292	0.00291
Other	0.00328	0.00310

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function as suppressor of malignant melanoma. It may exert its effects through interactions with the cytoskeleton.

Recessive Scores

• pRec: 0.129

Intolerance Scores

• rvis_EVS: 2.11
• rvis_percentile_EVS: 97.91

Haploinsufficiency Scores

• pHI: 0.365
• hipred: N
• hipred_score: 0.416
• ghis: 0.433

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Crybg1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); growth/size/body region phenotype

Gene ontology

• Biological process: biological_process
• Cellular component: cellular_component
• Molecular function: molecular_function;carbohydrate binding