CRYBA4

gene
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Summary

CRYBA4 (crystallin beta A4, HGNC:2396) is a protein-coding gene on chromosome 22q12.1, encoding Beta-crystallin A4 (P53673). Crystallins are the dominant structural components of the vertebrate eye lens.

Crystallins are separated into two classes: taxon-specific, or enzyme, and ubiquitous. The latter class constitutes the major proteins of vertebrate eye lens and maintains the transparency and refractive index of the lens. Since lens central fiber cells lose their nuclei during development, these crystallins are made and then retained throughout life, making them extremely stable proteins. Mammalian lens crystallins are divided into alpha, beta, and gamma families; beta and gamma crystallins are also considered as a superfamily. Alpha and beta families are further divided into acidic and basic groups. Seven protein regions exist in crystallins: four homologous motifs, a connecting peptide, and N- and C-terminal extensions. Beta-crystallins, the most heterogeneous, differ by the presence of the C-terminal extension (present in the basic group, none in the acidic group). Beta-crystallins form aggregates of different sizes and are able to self-associate to form dimers or to form heterodimers with other beta-crystallins. This gene, a beta acidic group member, is part of a gene cluster with beta-B1, beta-B2, and beta-B3.

Source: NCBI Gene 1413 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): cataract 23 (Definitive, GenCC) — +2 more curated relationships
  • Clinical variants (ClinVar): 222 total — 8 pathogenic, 11 likely-pathogenic
  • Phenotypes (HPO): 10
  • MANE Select transcript: NM_001886

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:2396
Approved symbolCRYBA4
Namecrystallin beta A4
Location22q12.1
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000196431
Ensembl biotypeprotein_coding
OMIM123631
Entrez1413

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000354760, ENST00000466315

RefSeq mRNA: 1 — MANE Select: NM_001886 NM_001886

CCDS: CCDS13841

Canonical transcript exons

ENST00000354760 — 6 exons

ExonStartEnd
ENSE000006519232662323426623352
ENSE000013892872662196326621986
ENSE000013918292663034026630669
ENSE000036019152662258526622635
ENSE000036802062662548126625622
ENSE000036904842662828826628430

Expression profiles

Bgee: expression breadth broad, 72 present calls, max score 81.40.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.4367 / max 334.3181, expressed in 54 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
1915120.436754

Top tissues by expression

206 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047381.40gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099172.82gold quality
frontal poleUBERON:000279567.98gold quality
paraflocculusUBERON:000535167.65gold quality
middle frontal gyrusUBERON:000270267.59gold quality
Brodmann (1909) area 10UBERON:001354166.79gold quality
endometrium epitheliumUBERON:000481159.40gold quality
cerebellar vermisUBERON:000472056.47gold quality
thymusUBERON:000237055.75silver quality
granulocyteCL:000009455.07gold quality
right testisUBERON:000453453.02gold quality
left testisUBERON:000453352.95gold quality
quadriceps femorisUBERON:000137752.71gold quality
testisUBERON:000047351.99gold quality
vastus lateralisUBERON:000137951.19gold quality
bone marrow cellCL:000209249.89gold quality
metanephric glomerulusUBERON:000473649.50gold quality
blood vessel layerUBERON:000479749.29gold quality
choroid plexus epitheliumUBERON:000391148.89gold quality
renal glomerulusUBERON:000007448.88gold quality
corpus epididymisUBERON:000435948.62gold quality
layer of synovial tissueUBERON:000761647.79gold quality
mucosa of transverse colonUBERON:000499147.60gold quality
spleenUBERON:000210647.45gold quality
periodontal ligamentUBERON:000826647.14gold quality
nephron tubuleUBERON:000123146.71gold quality
colonic epitheliumUBERON:000039746.37gold quality
prefrontal cortexUBERON:000045146.27gold quality
buccal mucosa cellCL:000233646.06gold quality
tracheaUBERON:000312645.55gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-MTAB-8060yes339.29
E-ANND-3no1.60

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

12 targeting CRYBA4, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-6798-5P100.0065.77699
HSA-MIR-6809-3P99.9171.453814
HSA-MIR-4753-3P99.9071.033786
HSA-MIR-430699.7270.503630
HSA-MIR-182799.6368.573265
HSA-MIR-211399.5871.221521
HSA-MIR-185-5P99.3568.602497
HSA-MIR-464499.3569.122514
HSA-MIR-130A-5P99.3370.262623
HSA-MIR-4717-3P99.0666.341072
HSA-MIR-570796.3466.1089
HSA-MIR-128192.9665.73260

Literature-anchored findings (GeneRIF, showing 6)

  • first report linking mutations in CRYBA4 to cataractogenesis and microphthalmia (PMID:16960806)
  • Novel missense mutation in CRYBA4 expands mutation spectrum of CRYBA4 and provides useful information to study of molecular pathogenesis of cataract and microcornea. (PMID:20577656)
  • rs2009066 located in the crystallin beta A4 (CRYBA4) gene was identified to be the most significantly associated with high myopia. (PMID:22792142)
  • CRYBA4 duplication and CRYBB1 partial duplication identified in a family with autosomal dominant congenital cataract. (PMID:28272538)
  • his study provides important reference value when narrowing down the number of pathogenic CRYBA4 nsSNPs and studying the pathogenesis of congenital cataracts. By using this method, we can easily find 44 high-risk pathogenic nsSNPs out of 157 CRYBA4 nsSNPs (PMID:31935276)
  • A novel missense variant c.71G > T (p.Gly24Val) of the CRYBA4 gene contributes to autosomal-dominant congenital cataract in a Chinese family. (PMID:35840783)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriocryba4ENSDARG00000024548
mus_musculusCryba4ENSMUSG00000066975
rattus_norvegicusCryba4ENSRNOG00000049770

Paralogs (14): CRYBG3 (ENSG00000080200), CRYBB3 (ENSG00000100053), CRYBB1 (ENSG00000100122), CRYBA1 (ENSG00000108255), CRYBG1 (ENSG00000112297), CRYGD (ENSG00000118231), CRYGN (ENSG00000127377), CRYGC (ENSG00000163254), CRYBA2 (ENSG00000163499), CRYGA (ENSG00000168582), CRYBG2 (ENSG00000176092), CRYGB (ENSG00000182187), CRYGS (ENSG00000213139), CRYBB2 (ENSG00000244752)

Protein

Protein identifiers

Beta-crystallin A4P53673 (reviewed: P53673)

Alternative names: Beta-A4 crystallin

All UniProt accessions (2): A0A097PIJ6, P53673

UniProt curated annotations — full annotation on UniProt →

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

Subunit / interactions. Homo/heterodimer, or complexes of higher-order. The structure of beta-crystallin oligomers seems to be stabilized through interactions between the N-terminal arms.

Disease relevance. Cataract 23, multiple types (CTRCT23) [MIM:610425] 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. CTRCT23 is a zonular cataract. Zonular or lamellar cataracts are opacities, broad or narrow, usually consisting of powdery white dots affecting only certain layers or zones between the cortex and nucleus of an otherwise clear lens. The opacity may be so dense as to render the entire central region of the lens completely opaque, or so translucent that vision is hardly if at all impeded. Zonular cataracts generally do not involve the embryonic nucleus, though sometimes they involve the fetal nucleus. Usually sharply separated from a clear cortex outside them, they may have projections from their outer edges known as riders or spokes. The disease is caused by variants affecting the gene represented in this entry.

Domain organisation. Has a two-domain beta-structure, folded into four very similar Greek key motifs.

Similarity. Belongs to the beta/gamma-crystallin family.

RefSeq proteins (1): NP_001877* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001064Beta/gamma_crystallinDomain
IPR011024G_crystallin-likeHomologous_superfamily
IPR050252Beta/Gamma-CrystallinFamily

Pfam: PF00030

UniProt features (36 total): strand 13, helix 7, sequence variant 5, domain 4, turn 2, region of interest 2, initiator methionine 1, chain 1, modified residue 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
3LWKX-RAY DIFFRACTION1.7

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P53673-F191.640.84

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 2

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

IDPathway
R-HSA-3371453Regulation of HSF1-mediated heat shock response
R-HSA-3371511HSF1 activation
R-HSA-3371568Attenuation phase
R-HSA-3371571HSF1-dependent transactivation

MSigDB gene sets: 102 (showing top): MORF_RAGE, MODULE_45, MODULE_16, MARTINEZ_RB1_TARGETS_UP, MODULE_205, MORF_FANCG, GOBP_SENSORY_PERCEPTION_OF_LIGHT_STIMULUS, MORF_PML, GOBP_SENSORY_PERCEPTION, MORF_IKBKG, GOBP_SENSORY_ORGAN_DEVELOPMENT, MODULE_18, MODULE_60, MORF_MT4, GOBP_LENS_DEVELOPMENT_IN_CAMERA_TYPE_EYE

GO Biological Process (3): lens development in camera-type eye (GO:0002088), visual perception (GO:0007601), camera-type eye development (GO:0043010)

GO Molecular Function (3): structural constituent of eye lens (GO:0005212), identical protein binding (GO:0042802), protein binding (GO:0005515)

GO Cellular Component (0):

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
Cellular response to heat stress3
HSF1-dependent transactivation1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
camera-type eye development1
anatomical structure development1
sensory perception of light stimulus1
eye development1
structural molecule activity1
protein binding1
binding1

Protein interactions and networks

STRING

503 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CRYBA4CRYAAP02489878
CRYBA4CRYABP02511808
CRYBA4GJA3Q9Y6H8761
CRYBA4GJA8P48165758
CRYBA4BFSP1Q12934748
CRYBA4BFSP2Q13515734
CRYBA4LIM2P55344675
CRYBA4TMEM114B3SHH9640
CRYBA4PITX3O75364633
CRYBA4HSF4Q9ULV5630
CRYBA4CHMP4BQ9H444626
CRYBA4GRIFINA4D1Z8625
CRYBA4FOXE3Q13461593
CRYBA4LGSNQ5TDP6586
CRYBA4MIPP30301553

IntAct

56 interactions, top by confidence:

ABTypeScore
CEP76CRYBA4psi-mi:“MI:0915”(physical association)0.780
CRYBA4CEP76psi-mi:“MI:0915”(physical association)0.780
CRYBA4CRYBB1psi-mi:“MI:0915”(physical association)0.730
CRYBA4CRYBB1psi-mi:“MI:0407”(direct interaction)0.730
CRYBA4CRYBB1psi-mi:“MI:0914”(association)0.730
CRYBB1CRYBA4psi-mi:“MI:0915”(physical association)0.730
CRYBA4CRYBA4psi-mi:“MI:0915”(physical association)0.630
CRYBA4CRYBA4psi-mi:“MI:0407”(direct interaction)0.630
CRYBA4IKZF3psi-mi:“MI:0915”(physical association)0.560
CRYBA4FHL5psi-mi:“MI:0915”(physical association)0.560
CRYBA4TRIP6psi-mi:“MI:0915”(physical association)0.560
CRYBA4C1orf94psi-mi:“MI:0915”(physical association)0.560
CRYBA4GLI1psi-mi:“MI:0915”(physical association)0.560
CRYBA4EFEMP1psi-mi:“MI:0915”(physical association)0.560
CRYBA4psi-mi:“MI:0915”(physical association)0.560
CRYBA4CCDC33psi-mi:“MI:0915”(physical association)0.560
CRYBA4STX11psi-mi:“MI:0915”(physical association)0.560
CRYBA4MIF4GDpsi-mi:“MI:0915”(physical association)0.560

BioGRID (42): CEP76 (Two-hybrid), C1orf94 (Two-hybrid), CCDC33 (Two-hybrid), CEP76 (Two-hybrid), EFEMP1 (Two-hybrid), FHL5 (Two-hybrid), GLI1 (Two-hybrid), IKZF3 (Two-hybrid), MIF4GD (Two-hybrid), PRR22 (Two-hybrid), STX11 (Two-hybrid), TRIP6 (Two-hybrid), EML5 (Affinity Capture-MS), DDB2 (Affinity Capture-MS), RBP4 (Affinity Capture-MS)

ESM2 similar proteins: A2IBY7, A3RLD7, A3RLD8, A3RLE1, A4L9I8, O35486, P02527, P02528, P02529, P02530, P02531, P04342, P04344, P04345, P06504, P07315, P07316, P07320, P08209, P0C5E9, P10065, P10066, P10067, P10068, P10112, P11844, P22914, P23005, P26444, P48646, P48647, P48649, P49152, P53673, P55164, P55940, P55941, Q03740, Q06254, Q06255

Diamond homologs: A2IBH5, A2IBY7, A2ICR5, A3RLD7, A3RLD8, A3RLE1, A3RLE2, A4L9I8, A4L9I9, A4QNB6, D3ZEG1, F6Q2R9, O35486, P02522, P02523, P02524, P02525, P02526, P02527, P02528, P02529, P02530, P02531, P04342, P04344, P04345, P05813, P06504, P07315, P07316, P07317, P07318, P07320, P07530, P08209, P0C5E9, P10042, P10043, P10065, P10066

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 18 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

GO biological processes:

GO termPartnersFoldFDR
visual perception526.5×5e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

222 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic8
Likely pathogenic11
Uncertain significance105
Likely benign48
Benign31

Top pathogenic / likely-pathogenic (19)

Variant IDHGVSClassification
16946NM_001886.3(CRYBA4):c.281T>C (p.Phe94Ser)Pathogenic
16947NM_001886.3(CRYBA4):c.206T>C (p.Leu69Pro)Pathogenic
427575NM_001886.3(CRYBA4):c.190G>T (p.Gly64Trp)Pathogenic
427749NM_001887.4(CRYBB1):c.387C>A (p.Ser129Arg)Pathogenic
4796486NM_001887.4(CRYBB1):c.576-637_587delPathogenic
4796487NM_001886.3(CRYBA4):c.220T>C (p.Tyr74His)Pathogenic
574493NM_001887.4(CRYBB1):c.585del (p.Tyr196fs)Pathogenic
8687NM_001887.4(CRYBB1):c.658G>T (p.Gly220Ter)Pathogenic
1176010NM_001887.4(CRYBB1):c.211G>A (p.Gly71Ser)Likely pathogenic
1343240NM_001886.3(CRYBA4):c.277T>C (p.Ser93Pro)Likely pathogenic
1679950NM_001887.4(CRYBB1):c.419G>C (p.Arg140Pro)Likely pathogenic
217329NM_001887.4(CRYBB1):c.368G>A (p.Arg123His)Likely pathogenic
2737022NM_001887.4(CRYBB1):c.698G>A (p.Arg233His)Likely pathogenic
3065113NM_001887.4(CRYBB1):c.2T>A (p.Met1Lys)Likely pathogenic
3587868NM_001887.4(CRYBB1):c.387C>G (p.Ser129Arg)Likely pathogenic
369847hg19chr22:g.26995597_27074524dupLikely pathogenic
3779548NM_001887.4(CRYBB1):c.482del (p.Gly161fs)Likely pathogenic
4085351NM_001887.4(CRYBB1):c.601_604del (p.Tyr201fs)Likely pathogenic
965311NM_001886.3(CRYBA4):c.198_200del (p.Gln66_Tyr67delinsHis)Likely pathogenic

SpliceAI

523 predictions. Top by Δscore:

VariantEffectΔscore
22:26623226:T:Aacceptor_gain1.0000
22:26623342:C:Gdonor_gain1.0000
22:26623348:GGAGC:Gdonor_gain1.0000
22:26623349:GAGCG:Gdonor_gain1.0000
22:26623351:GC:Gdonor_gain1.0000
22:26623353:G:GGdonor_gain1.0000
22:26625623:G:GGdonor_gain1.0000
22:26628283:TGTA:Tacceptor_loss1.0000
22:26628284:GTA:Gacceptor_loss1.0000
22:26628285:TAG:Tacceptor_loss1.0000
22:26628286:A:AGacceptor_gain1.0000
22:26628287:G:Aacceptor_loss1.0000
22:26628287:G:GTacceptor_gain1.0000
22:26628287:GA:Gacceptor_gain1.0000
22:26628287:GAAC:Gacceptor_gain1.0000
22:26628287:GAACC:Gacceptor_gain1.0000
22:26628347:A:Tdonor_gain1.0000
22:26628390:G:Tdonor_gain1.0000
22:26628399:G:GTdonor_gain1.0000
22:26628402:G:GGdonor_gain1.0000
22:26628426:GGGGC:Gdonor_gain1.0000
22:26628427:GGGC:Gdonor_gain1.0000
22:26628427:GGGCG:Gdonor_gain1.0000
22:26628428:GGC:Gdonor_gain1.0000
22:26628428:GGCG:Gdonor_gain1.0000
22:26628429:GC:Gdonor_gain1.0000
22:26628429:GCG:Gdonor_gain1.0000
22:26628431:G:GGdonor_gain1.0000
22:26630335:TCCA:Tacceptor_loss1.0000
22:26630337:CA:Cacceptor_loss1.0000

AlphaMissense

1283 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
22:26625482:T:AW54R0.993
22:26625482:T:CW54R0.993
22:26625491:T:CF57L0.992
22:26625493:T:AF57L0.992
22:26625493:T:GF57L0.992
22:26625603:T:CF94S0.991
22:26630464:A:CS190R0.991
22:26630465:G:TS190I0.991
22:26630466:C:AS190R0.991
22:26630466:C:GS190R0.991
22:26630341:T:AW149R0.990
22:26630341:T:CW149R0.990
22:26630471:G:CR192P0.989
22:26625489:G:AG56D0.988
22:26628315:T:CF110L0.986
22:26628317:C:AF110L0.986
22:26628317:C:GF110L0.986
22:26630347:T:CC151R0.986
22:26630475:G:CR193S0.985
22:26630475:G:TR193S0.985
22:26625606:G:CR95P0.984
22:26630431:T:AW179R0.984
22:26630431:T:CW179R0.984
22:26625488:G:CG56R0.983
22:26625542:T:GY74D0.983
22:26628418:T:AV144D0.983
22:26630349:C:GC151W0.982
22:26630372:G:AG159E0.981
22:26630474:G:TR193M0.981
22:26623330:T:CS46P0.980

dbSNP variants (sampled 300 via entrez): RS1000021247 (22:26630371 G>A), RS1000065306 (22:26621333 T>C), RS1000106932 (22:26607990 C>A,G,T), RS1000142670 (22:26589581 C>T), RS1000196878 (22:26589736 C>A), RS1000307065 (22:26612508 CCCA>C), RS1000330419 (22:26595326 C>A,T), RS1000342443 (22:26623624 T>C), RS1000396697 (22:26630436 C>A), RS1000431288 (22:26595533 C>G,T), RS1000473720 (22:26589264 C>T), RS1000489042 (22:26611486 G>T), RS1000612265 (22:26613604 A>G), RS1000643517 (22:26613849 CA>C), RS1000675947 (22:26619852 G>A)

Disease associations

OMIM: gene MIM:123631 | disease phenotypes: MIM:610425, MIM:611544, MIM:601371

GenCC curated gene-disease

DiseaseClassificationInheritance
cataract 23DefinitiveAutosomal dominant
cataract - microcornea syndromeSupportiveAutosomal dominant
early-onset lamellar cataractSupportiveAutosomal dominant

Mondo (5): cataract 23 (MONDO:0012489), cataract 17 multiple types (MONDO:0012688), early-onset non-syndromic cataract (MONDO:0011060), cataract - microcornea syndrome (MONDO:0015300), early-onset lamellar cataract (MONDO:0018611)

Orphanet (1): Early onset non-syndromic cataract (Orphanet:91492)

HPO phenotypes

10 total (10 of 10 shown, HPO-id order):

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0000482Microcornea
HP:0000518Cataract
HP:0000545Myopia
HP:0000612Iris coloboma
HP:0000639Nystagmus
HP:0001131Corneal dystrophy
HP:0007957Corneal opacity
HP:0007971Lamellar cataract
HP:0100018Nuclear cataract

GWAS associations

0 associations (top):

MeSH disease descriptors (2)

DescriptorNameTree numbers
C538287Cataract microcornea syndrome (supp.)
C566923Cataract, Congenital Nuclear, Autosomal Recessive 3 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

16 total (human), top 16 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression, decreases expression, affects expression, increases methylation8
mercuric bromidedecreases expression, affects cotreatment2
belinostatdecreases expression, affects cotreatment2
Panobinostataffects cotreatment, decreases expression2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
methylmercuric chloridedecreases expression1
trichostatin Adecreases expression1
butyraldehydedecreases expression1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamidedecreases expression, affects cotreatment1
dorsomorphinaffects cotreatment, decreases expression1
Acetaminophendecreases expression1
Benzo(a)pyreneaffects methylation1
Hydralazineincreases expression, affects cotreatment1
Aflatoxin B1increases methylation1
Cadmium Chlorideincreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.