GeneBe

CRYBB3

crystallin beta B3, the group of Beta-gamma crystallins

Basic information

Region (hg38): 22:25199858-25207359

Previous symbols: [ "CRYB3" ]

Links

ENSG00000100053 ∙ NCBI:1417 ∙ OMIM:123630 ∙ HGNC:2400 ∙ Uniprot:P26998 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • cataract 22 multiple types (Definitive), mode of inheritance: AR
  • cataract 22 multiple types (Moderate), mode of inheritance: Semidominant
  • early-onset anterior polar cataract (Supportive), mode of inheritance: AD
  • early-onset nuclear cataract (Supportive), mode of inheritance: AD
  • cataract 22 multiple types (Strong), mode of inheritance: AR
  • cataract 22 multiple types (Strong), mode of inheritance: AD
  • cataract 22 multiple types (Moderate), mode of inheritance: AD
  • cataract 22 multiple types (Moderate), mode of inheritance: AR
  • early-onset non-syndromic cataract (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Cataract 22, multiple typesAD/ARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingOphthalmologic15914629; 27326458; 28418495; 23508780

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CRYBB3 gene.

  • Cataract_22_multiple_types (54 variants)
  • Inborn_genetic_diseases (46 variants)
  • not_provided (21 variants)
  • CRYBB3-related_disorder (4 variants)
  • Developmental_cataract (2 variants)
  • Congenital_nuclear_cataract (2 variants)
  • Cataract (1 variants)
  • Microphthalmia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CRYBB3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004076.5. 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.

EffectPLPVUSLBBSum
synonymous
4
clinvar
8
clinvar
1
clinvar
 13
missense
3
clinvar
3
clinvar
57
clinvar
8
clinvar
 71
nonsense
1
clinvar
 1
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
1
clinvar
 1
Total 3 3 61 18 1

Highest pathogenic variant AF is 0.0000068428

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CRYBB3protein_codingprotein_codingENST00000215855 57514
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
3.58e-110.025512535423921257480.00157
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.1261511471.030.00001111392
Missense in Polyphen4652.7820.87151521
Synonymous-0.4615853.71.080.00000386392
Loss of Function-0.4621513.21.147.74e-7115

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.005900.00580
Ashkenazi Jewish0.01900.0190
East Asian0.001690.00169
Finnish0.00004620.0000462
European (Non-Finnish)0.0004340.000431
Middle Eastern0.001690.00169
South Asian0.0002940.000294
Other0.002130.00212

dbNSFP

Source: dbNSFP

Function
FUNCTION: Crystallins are the dominant structural components of the vertebrate eye lens.;
Disease
DISEASE: Cataract 22, multiple types (CTRCT22) [MIM:609741]: 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. CTRCT22 includes nuclear cataract among others. Nuclear cataracts affect the central nucleus of the eye, and are often not highly visually significant. The density of the opacities varies greatly from fine dots to a dense, white and chalk-like, central cataract. The condition is usually bilateral. Nuclear cataracts are often combined with opacified cortical fibers encircling the nuclear opacity, which are referred to as cortical riders. {ECO:0000269|PubMed:15914629, ECO:0000269|PubMed:23508780}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.125

Intolerance Scores

loftool
0.808
rvis_EVS
0.82
rvis_percentile_EVS
87.99

Haploinsufficiency Scores

pHI
0.121
hipred
N
hipred_score
0.284
ghis
0.483

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.376

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Crybb3
Phenotype
skeleton phenotype;

Gene ontology

Biological process
visual perception
Cellular component
Molecular function
structural constituent of eye lens;protein binding