CRYBA2

crystallin beta A2, the group of Beta-gamma crystallins

Basic information

Region (hg38): 2:218990189-218993422

Links

ENSG00000163499 ∙ NCBI:1412 ∙ OMIM:600836 ∙ HGNC:2395 ∙ Uniprot:P53672 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• cataract 42 (Limited), mode of inheritance: Semidominant
• early-onset anterior polar cataract (Supportive), mode of inheritance: AD
• early-onset nuclear cataract (Supportive), mode of inheritance: AD
• cataract 42 (Limited), mode of inheritance: AD
• cataract 42 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cataract 42	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	23508780

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CRYBA2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CRYBA2 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			9		1	10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				2	2	4
Total	0	0	9	2	3

Variants in CRYBA2

This is a list of pathogenic ClinVar variants found in the CRYBA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-218990275-A-G		not specified	Uncertain significance (Mar 28, 2023)
2-218990305-C-T		not specified	Uncertain significance (Jun 07, 2023)
2-218990314-C-T		CRYBA2-related disorder	Uncertain significance (Sep 05, 2024)
2-218990340-C-T		CRYBA2-related disorder	Benign (Dec 22, 2023)
2-218990382-T-C		not specified	Uncertain significance (Jun 23, 2021)
2-218990937-A-T		not specified	Uncertain significance (May 28, 2024)
2-218990978-C-T		CRYBA2-related disorder	Uncertain significance (Aug 25, 2023)
2-218990979-G-A		CRYBA2-related disorder	Uncertain significance (Sep 20, 2024)
2-218991010-A-G			Benign (Sep 18, 2018)
2-218991975-T-C			Benign (Jul 31, 2018)
2-218992118-C-T		not specified	Uncertain significance (Mar 07, 2024)
2-218992119-G-A		not specified	Uncertain significance (Jul 14, 2023)
2-218992162-C-A		not specified	Uncertain significance (Dec 01, 2023)
2-218992167-C-T		CRYBA2-related disorder • not specified	Uncertain significance (Mar 07, 2023)
2-218992208-T-C		not specified	Uncertain significance (Jan 18, 2023)
2-218993096-A-T		CRYBA2-related disorder	Uncertain significance (Jul 10, 2024)
2-218993104-G-T		not specified	Uncertain significance (Apr 23, 2024)
2-218993228-C-G			Likely benign (Dec 24, 2019)
2-218993399-G-A			Likely benign (Nov 22, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CRYBA2	protein_coding	protein_coding	ENST00000295728	4	3233

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000195	0.734	125636	0	109	125745	0.000434

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.380	128	116	1.10	0.00000548	1278
Missense in Polyphen		38	42.592	0.89219		528
Synonymous	-0.238	50	47.9	1.04	0.00000233	377
Loss of Function	0.976	7	10.4	0.673	4.59e-7	99

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000701	0.000701
Ashkenazi Jewish	0.00199	0.00199
East Asian	0.000598	0.000598
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000447	0.000440
Middle Eastern	0.000598	0.000598
South Asian	0.0000327	0.0000327
Other	0.000494	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Crystallins are the dominant structural components of the vertebrate eye lens.
• Disease: DISEASE: Cataract 42 (CTRCT42) [MIM:115900]: 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. {ECO:0000269|PubMed:23508780}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.122

Intolerance Scores

• loftool: 0.570
• rvis_EVS: -0.18
• rvis_percentile_EVS: 39.95

Haploinsufficiency Scores

• pHI: 0.140
• hipred: N
• hipred_score: 0.299
• ghis: 0.398

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.719

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cryba2
• Phenotype: vision/eye phenotype

Gene ontology

• Biological process: lens development in camera-type eye;biological_process
• Cellular component: cellular_component
• Molecular function: molecular_function;structural constituent of eye lens;protein binding;protein homodimerization activity