Human Gene CRYGD (uc002vcn.4) Description and Page Index
  Description: Homo sapiens crystallin, gamma D (CRYGD), mRNA.
RefSeq Summary (NM_006891): 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. Gamma-crystallins are a homogeneous group of highly symmetrical, monomeric proteins typically lacking connecting peptides and terminal extensions. They are differentially regulated after early development. Four gamma-crystallin genes (gamma-A through gamma-D) and three pseudogenes (gamma-E, gamma-F, gamma-G) are tandemly organized in a genomic segment as a gene cluster. Whether due to aging or mutations in specific genes, gamma-crystallins have been involved in cataract formation. [provided by RefSeq, Jul 2008]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: BC117338.1, CD676210.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1968968, SAMEA2145245 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000264376.5/ ENSP00000264376.4 RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr2:208,986,331-208,989,313 Size: 2,983 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg19 chr2:208,986,397-208,989,197 Size: 2,801 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:208,986,331-208,989,313)mRNA (may differ from genome)Protein (174 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkHGNCHPRDLynxMGIneXtProt
OMIMPubMedStanford SOURCETreefamUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: CRGD_HUMAN
DESCRIPTION: RecName: Full=Gamma-crystallin D; AltName: Full=Gamma-D-crystallin; AltName: Full=Gamma-crystallin 4;
FUNCTION: Crystallins are the dominant structural components of the vertebrate eye lens.
SUBUNIT: Monomer (By similarity).
DOMAIN: Has a two-domain beta-structure, folded into four very similar Greek key motifs.
DISEASE: Defects in CRYGD are a cause of cataract autosomal dominant (ADC) [MIM:604219]. Cataract is 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. Cataract is the most common treatable cause of visual disability in childhood.
DISEASE: Defects in CRYGD are the cause of cataract congenital non-nuclear polymorphic autosomal dominant (CCP) [MIM:601286]; also known as polymorphic congenital cataract. A congenital cataract characterized by a non-progressive phenotype and partial opacity that has a variable location between the fetal nucleus of the lens and the equator. The fetal nucleus is normal. The opacities are irregular and look similar to a bunch of grapes and may be present simultaneously in different lens layers.
DISEASE: Defects in CRYGD are the cause of cataract congenital cerulean type 3 (CCA3) [MIM:608983]; also known as congenital cataract blue dot type 3. A cerulean form of autosomal dominant congenital cataract. Cerulean cataract is characterized by peripheral bluish and white opacifications organized in concentric layers with occasional central lesions arranged radially. The opacities are observed in the superficial layers of the fetal nucleus as well as the adult nucleus of the lens. Involvement is usually bilateral. Visual acuity is only mildly reduced in childhood. In adulthood, the opacifications may progress, making lens extraction necessary. Histologically the lesions are described as fusiform cavities between lens fibers which contain a deeply staining granular material. Although the lesions may take on various colors, a dull blue is the most common appearance and is responsible for the designation cerulean cataract.
DISEASE: Defects in CRYGD are the cause of cataract crystalline aculeiform (CACA) [MIM:115700]. A congenital crystalline cataract characterized by fiberglass-like or needle-like crystals projecting in different directions, through or close to the axial region of the lens. The opacity causes a variable degree of vision loss.
SIMILARITY: Belongs to the beta/gamma-crystallin family.
SIMILARITY: Contains 4 beta/gamma crystallin 'Greek key' domains.
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/CRYGD";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CRYGD
CDC HuGE Published Literature: CRYGD
Positive Disease Associations: smoking cessation
Related Studies:
  1. smoking cessation
    Uhl ,et al. Pharmacogenomics 2010, Genome-wide association for smoking cessation success: participants in the Patch in Practice trial of nicotine replacement , Pharmacogenomics 2010 11- 3 : 357-67. [PubMed 20235792]

-  MalaCards Disease Associations
  MalaCards Gene Search: CRYGD
Diseases sorted by gene-association score: cataract 4, multiple types* (1230), cataract 29, coralliform* (350), cerulean cataract* (213), cataract 9, multiple types* (188), cataract microcornea syndrome* (157), cataract 16, multiple types* (124), cataract 30, pulverulent* (117), early-onset nuclear cataract* (117), cataract, autosomal dominant congenital 4* (100), cataract (32), posterior polar cataract (11), nuclear senile cataract (9), acute cholangitis (7), propionicacidemia (5)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 3.50 RPKM in Ovary
Total median expression: 13.81 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -31.30116-0.270 Picture PostScript Text
3' UTR -8.4066-0.127 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001064 - Beta/gamma_crystallin
IPR011024 - G_crystallin-rel

Pfam Domains:
PF00030 - Beta/Gamma crystallin

SCOP Domains:
49695 - gamma-Crystallin-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help

1H4A
- X-ray

1HK0
- X-ray

1LD0
- Model
To conserve bandwidth, only the images from the first 3 structures are shown.
2G98 - X-ray 2KFB - NMR MuPIT 2KLJ - Other MuPIT


ModBase Predicted Comparative 3D Structure on P07320
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005212 structural constituent of eye lens
GO:0005515 protein binding

Biological Process:
GO:0002088 lens development in camera-type eye
GO:0007601 visual perception
GO:0034614 cellular response to reactive oxygen species
GO:0050896 response to stimulus
GO:0070306 lens fiber cell differentiation

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm


-  Descriptions from all associated GenBank mRNAs
  U66583 - Human gammaD-crystallin (CRYGD) mRNA, complete cds.
BC117338 - Homo sapiens crystallin, gamma D, mRNA (cDNA clone MGC:150947 IMAGE:40125889), complete cds.
BC117340 - Homo sapiens crystallin, gamma D, mRNA (cDNA clone MGC:150949 IMAGE:40125891), complete cds.
JD254158 - Sequence 235182 from Patent EP1572962.
KT966392 - Homo sapiens gamma-crystallin D (CRYGD) mRNA, complete cds.
KR711628 - Synthetic construct Homo sapiens clone CCSBHm_00027883 CRYGD (CRYGD) mRNA, encodes complete protein.
HQ258094 - Synthetic construct Homo sapiens clone IMAGE:100072403 crystallin, gamma D (CRYGD) gene, encodes complete protein.
KJ896652 - Synthetic construct Homo sapiens clone ccsbBroadEn_06046 CRYGD gene, encodes complete protein.
KR711627 - Synthetic construct Homo sapiens clone CCSBHm_00027881 CRYGD (CRYGD) mRNA, encodes complete protein.
KR711629 - Synthetic construct Homo sapiens clone CCSBHm_00027887 CRYGD (CRYGD) mRNA, encodes complete protein.
KR711630 - Synthetic construct Homo sapiens clone CCSBHm_00027888 CRYGD (CRYGD) mRNA, encodes complete protein.

-  Other Names for This Gene
  Alternate Gene Symbols: CRGD_HUMAN, CRYG4, NM_006891, NP_008822, P07320, Q17RF7, Q53R51, Q99681
UCSC ID: uc002vcn.4
RefSeq Accession: NM_006891
Protein: P07320 (aka CRGD_HUMAN)
CCDS: CCDS2378.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_006891.3
exon count: 3CDS single in 3' UTR: no RNA size: 724
ORF size: 525CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1250.00frame shift in genome: no % Coverage: 97.65
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.