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Aliases for CRYM Gene

Aliases for CRYM Gene

  • Crystallin Mu 2 3 5
  • Thiomorpholine-Carboxylate Dehydrogenase 2 3
  • THBP 3 4
  • NADP-Regulated Thyroid-Hormone Binding Protein 3
  • NADP-Regulated Thyroid-Hormone-Binding Protein 4
  • Ketimine Reductase Mu-Crystallin 3
  • Mu-Crystallin Homolog 3
  • Crystallin, Mu 2
  • EC 1.5.1.25 4
  • DFNA40 3

External Ids for CRYM Gene

Previous GeneCards Identifiers for CRYM Gene

  • GC16M020678
  • GC16M021278
  • GC16M021236
  • GC16M021177
  • GC16M019805
  • GC16M021269

Summaries for CRYM Gene

Entrez Gene Summary for CRYM Gene

  • Crystallins are separated into two classes: taxon-specific and ubiquitous. The former class is also called phylogenetically-restricted crystallins. The latter class constitutes the major proteins of vertebrate eye lens and maintains the transparency and refractive index of the lens. This gene encodes a taxon-specific crystallin protein that binds NADPH and has sequence similarity to bacterial ornithine cyclodeaminases. The encoded protein does not perform a structural role in lens tissue, and instead it binds thyroid hormone for possible regulatory or developmental roles. Mutations in this gene have been associated with autosomal dominant non-syndromic deafness. [provided by RefSeq, Sep 2014]

GeneCards Summary for CRYM Gene

CRYM (Crystallin Mu) is a Protein Coding gene. Diseases associated with CRYM include Deafness, Autosomal Dominant 40 and Autosomal Dominant Non-Syndromic Sensorineural Deafness Type Dfna. Among its related pathways are Viral mRNA Translation and Metabolism. Gene Ontology (GO) annotations related to this gene include protein homodimerization activity and NADP binding.

UniProtKB/Swiss-Prot for CRYM Gene

  • Specifically catalyzes the reduction of imine bonds in brain substrates that may include cystathionine ketimine (CysK) and lanthionine ketimine (LK). Binds thyroid hormone which is a strong reversible inhibitor. Presumably involved in the regulation of the free intracellular concentration of triiodothyronine and access to its nuclear receptors.

Gene Wiki entry for CRYM Gene

Additional gene information for CRYM Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CRYM Gene

Genomics for CRYM Gene

GeneHancer (GH) Regulatory Elements for CRYM Gene

Promoters and enhancers for CRYM Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH16I021300 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 565.2 +1.1 1090 3.9 CLOCK MLX ZFP64 DMAP1 YY1 SLC30A9 E2F8 ZNF143 ZNF263 SP3 CRYM GC16M021264 CRYM-AS1 RRN3P1 ENSG00000260306 C16orf52 TMEM159 DNAH3 EEF2K ENSG00000283421
GH16I021278 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 555.9 +24.8 24755 0.4 ARID4B ZNF48 GLIS2 ZNF143 KLF7 SP3 SP5 MXD4 REST KAT8 CRYM DNAH3 TMEM159 LOC105371125 GC16M021264 LOC105371124
GH16I021263 Enhancer 1.1 Ensembl ENCODE 46.8 +38.8 38787 1.7 HDAC1 ELF3 PKNOX1 FOXA2 ARID4B DMAP1 RAD21 THRB ZNF48 RARA CRYM ANKS4B DNAH3 TMEM159 ZP2 LOC105371124 LOC105371125 GC16M021264
GH16I020896 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 7.5 +400.5 400480 11.5 CLOCK DMAP1 YY1 SLC30A9 E2F8 ZNF143 SP3 NFYC MEF2D GLIS1 DCUN1D3 LYRM1 THUMPD1 ACSM3 SMG1P3 ACSM1 CRYM ERI2 PIR35456 GC16P020829
GH16I021598 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 6.9 -296.4 -296431 4.6 CLOCK MLX ZFP64 DMAP1 IRF4 YY1 ZNF213 E2F8 ZNF143 SP3 METTL9 LOC101927814 IGSF6 NPIPB5 REXO5 NPIPB4 NPIPB3 THUMPD1 MFSD13B CRYM
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around CRYM on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CRYM gene promoter:

Genomic Locations for CRYM Gene

Genomic Locations for CRYM Gene
chr16:21,238,874-21,303,136
(GRCh38/hg38)
Size:
64,263 bases
Orientation:
Minus strand
chr16:21,250,195-21,314,404
(GRCh37/hg19)

Genomic View for CRYM Gene

Genes around CRYM on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CRYM Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CRYM Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CRYM Gene

Proteins for CRYM Gene

  • Protein details for CRYM Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q14894-CRYM_HUMAN
    Recommended name:
    Ketimine reductase mu-crystallin
    Protein Accession:
    Q14894
    Secondary Accessions:
    • D5MNX0
    • Q5HYB7

    Protein attributes for CRYM Gene

    Size:
    314 amino acids
    Molecular mass:
    33776 Da
    Cofactor:
    Name=NAD(+); Xref=ChEBI:CHEBI:57540; Name=NADP(+); Xref=ChEBI:CHEBI:58349;
    Quaternary structure:
    • Homodimer.

    Three dimensional structures from OCA and Proteopedia for CRYM Gene

neXtProt entry for CRYM Gene

Post-translational modifications for CRYM Gene

No Post-translational modifications

Other Protein References for CRYM Gene

No data available for DME Specific Peptides for CRYM Gene

Domains & Families for CRYM Gene

Gene Families for CRYM Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted intracellular proteins

Protein Domains for CRYM Gene

Suggested Antigen Peptide Sequences for CRYM Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q14894

UniProtKB/Swiss-Prot:

CRYM_HUMAN :
  • Belongs to the ornithine cyclodeaminase/mu-crystallin family.
Family:
  • Belongs to the ornithine cyclodeaminase/mu-crystallin family.
genes like me logo Genes that share domains with CRYM: view

Function for CRYM Gene

Molecular function for CRYM Gene

GENATLAS Biochemistry:
crystallin,mu polypeptide
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=47 uM for 3,4-dehydro-thiomorpholine-3-carboxylate (at pH 5.0 and 37 degrees Celsius) {ECO:0000269 PubMed:21332720}; KM=3.6 uM for NADH (at pH 5.0 and 37 degrees Celsius) {ECO:0000269 PubMed:21332720}; Vmax=9.6 umol/min/mg enzyme with 3,4-dehydro-thiomorpholine-3- carboxylate as substrate (at pH 5.0 and 37 degrees Celsius) {ECO:0000269 PubMed:21332720}; pH dependence: Optimum pH is 4.5. {ECO:0000269 PubMed:21332720};
UniProtKB/Swiss-Prot CatalyticActivity:
Thiomorpholine 3-carboxylate + NAD(P)(+) = 3,4-dehydro-thiomorpholine-3-carboxylate + NAD(P)H.
UniProtKB/Swiss-Prot Function:
Specifically catalyzes the reduction of imine bonds in brain substrates that may include cystathionine ketimine (CysK) and lanthionine ketimine (LK). Binds thyroid hormone which is a strong reversible inhibitor. Presumably involved in the regulation of the free intracellular concentration of triiodothyronine and access to its nuclear receptors.

Enzyme Numbers (IUBMB) for CRYM Gene

Gene Ontology (GO) - Molecular Function for CRYM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003714 transcription corepressor activity IMP 11897713
GO:0005515 protein binding IPI 21044950
GO:0016491 oxidoreductase activity IEA --
GO:0016639 oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor IBA --
GO:0042562 hormone binding IEA --
genes like me logo Genes that share ontologies with CRYM: view
genes like me logo Genes that share phenotypes with CRYM: view

Human Phenotype Ontology for CRYM Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for CRYM Gene

MGI Knock Outs for CRYM:

Animal Model Products

Clone Products

  • Addgene plasmids for CRYM

No data available for Phenotypes From GWAS Catalog , miRNA , Transcription Factor Targets and HOMER Transcription for CRYM Gene

Localization for CRYM Gene

Subcellular locations from UniProtKB/Swiss-Prot for CRYM Gene

Cytoplasm.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CRYM gene
Compartment Confidence
extracellular 5
cytosol 5
peroxisome 4
nucleus 3
mitochondrion 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for CRYM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005737 cytoplasm IEA,IDA 12471561
GO:0005739 mitochondrion IEA --
GO:0005782 peroxisomal matrix TAS --
GO:0005829 cytosol IDA --
genes like me logo Genes that share ontologies with CRYM: view

Pathways & Interactions for CRYM Gene

genes like me logo Genes that share pathways with CRYM: view

Gene Ontology (GO) - Biological Process for CRYM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IMP 11897713
GO:0006554 lysine catabolic process TAS --
GO:0007605 sensory perception of sound IMP 12471561
GO:0042403 thyroid hormone metabolic process IBA --
GO:0055114 oxidation-reduction process IEA --
genes like me logo Genes that share ontologies with CRYM: view

No data available for SIGNOR curated interactions for CRYM Gene

Drugs & Compounds for CRYM Gene

(8) Drugs for CRYM Gene - From: DrugBank and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
NRP409 Investigational Pharma Target 0

(2) Additional Compounds for CRYM Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Thiomorpholine 3-carboxylate
genes like me logo Genes that share compounds with CRYM: view

Transcripts for CRYM Gene

Unigene Clusters for CRYM Gene

Crystallin, mu:
Representative Sequences:

Clone Products

  • Addgene plasmids for CRYM

Alternative Splicing Database (ASD) splice patterns (SP) for CRYM Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8
SP1: - - -
SP2: - - -
SP3:
SP4:

Relevant External Links for CRYM Gene

GeneLoc Exon Structure for
CRYM
ECgene alternative splicing isoforms for
CRYM

Expression for CRYM Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CRYM Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CRYM Gene

This gene is overexpressed in Brain - Nucleus accumbens (basal ganglia) (x8.1), Brain - Caudate (basal ganglia) (x4.2), Brain - Frontal Cortex (BA9) (x4.2), Brain - Cerebellar Hemisphere (x4.1), and Brain - Cortex (x4.1).

Protein differential expression in normal tissues from HIPED for CRYM Gene

This gene is overexpressed in Retina (23.1) and Brain (10.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for CRYM Gene



NURSA nuclear receptor signaling pathways regulating expression of CRYM Gene:

CRYM

SOURCE GeneReport for Unigene cluster for CRYM Gene:

Hs.924

mRNA Expression by UniProt/SwissProt for CRYM Gene:

Q14894-CRYM_HUMAN
Tissue specificity: Expressed in neural tissue, muscle and kidney.

Evidence on tissue expression from TISSUES for CRYM Gene

  • Nervous system(4.8)
  • Eye(4.3)
  • Liver(4.1)
  • Heart(2)
  • Kidney(2)
  • Thyroid gland(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for CRYM Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • nervous
Organs:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • head
  • inner ear
  • middle ear
  • outer ear
Thorax:
  • heart
  • heart valve
Limb:
  • forearm
General:
  • peripheral nerve
  • peripheral nervous system
genes like me logo Genes that share expression patterns with CRYM: view

No data available for Protein tissue co-expression partners for CRYM Gene

Orthologs for CRYM Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for CRYM Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CRYM 33 34
  • 99.47 (n)
dog
(Canis familiaris)
Mammalia CRYM 33 34
  • 91.3 (n)
cow
(Bos Taurus)
Mammalia CRYM 33 34
  • 89.38 (n)
oppossum
(Monodelphis domestica)
Mammalia CRYM 34
  • 88 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia CRYM 34
  • 88 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Crym 33 16 34
  • 87.01 (n)
rat
(Rattus norvegicus)
Mammalia Crym 33
  • 86.58 (n)
chicken
(Gallus gallus)
Aves CRYM 33 34
  • 70.09 (n)
lizard
(Anolis carolinensis)
Reptilia CRYM 34
  • 80 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia crym 33
  • 67.42 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.24695 33
zebrafish
(Danio rerio)
Actinopterygii crym 33 34
  • 60.43 (n)
Dr.22409 33
fruit fly
(Drosophila melanogaster)
Insecta CG4872 33 34
  • 49.78 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP011137 33
  • 47.43 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes -- 36
thale cress
(Arabidopsis thaliana)
eudicotyledons AT5G52810 33
  • 46.38 (n)
rice
(Oryza sativa)
Liliopsida Os10g0533200 33
  • 49.12 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 45 (a)
OneToOne
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPAP11E10.01 33
  • 41.96 (n)
Species where no ortholog for CRYM was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for CRYM Gene

ENSEMBL:
Gene Tree for CRYM (if available)
TreeFam:
Gene Tree for CRYM (if available)

Paralogs for CRYM Gene

No data available for Paralogs for CRYM Gene

Variants for CRYM Gene

Sequence variations from dbSNP and Humsavar for CRYM Gene

SNP ID Clin Chr 16 pos Variation AA Info Type
rs104894509 pathogenic, Deafness, autosomal dominant 40 21,258,781(-) T/A stop_lost, terminator_codon_variant
rs104894512 pathogenic, Deafness, autosomal dominant 40, Deafness, autosomal dominant, 40 (DFNA40) [MIM:616357] 21,258,785(-) T/C/G coding_sequence_variant, missense_variant
rs149797560 uncertain-significance, Deafness, autosomal dominant 40, not provided 21,278,244(-) C/A coding_sequence_variant, missense_variant
rs144588424 conflicting-interpretations-of-pathogenicity, not specified 21,261,327(-) A/G coding_sequence_variant, synonymous_variant
rs386789728 conflicting-interpretations-of-pathogenicity, not specified 21,267,703(-) TC/AA coding_sequence_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for CRYM Gene

Variant ID Type Subtype PubMed ID
esv2714068 CNV deletion 23290073
esv2758636 CNV gain+loss 17122850
esv34235 CNV gain 17911159
esv3638164 CNV gain 21293372
esv3638165 CNV gain 21293372
nsv436835 CNV insertion 17901297
nsv526247 CNV loss 19592680
nsv571623 CNV gain 21841781

Variation tolerance for CRYM Gene

Residual Variation Intolerance Score: 57.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.17; 39.35% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CRYM Gene

Human Gene Mutation Database (HGMD)
CRYM
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CRYM

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CRYM Gene

Disorders for CRYM Gene

MalaCards: The human disease database

(6) MalaCards diseases for CRYM Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
deafness, autosomal dominant 40
  • dfna40
autosomal dominant non-syndromic sensorineural deafness type dfna
  • autosomal dominant isolated neurosensory deafness type dfna
retinitis pigmentosa 22
  • rp22
nonsyndromic deafness
  • nonsyndromic hearing loss
facioscapulohumeral muscular dystrophy 1
  • fmd
- elite association - COSMIC cancer census association via MalaCards
Search CRYM in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

CRYM_HUMAN
  • Deafness, autosomal dominant, 40 (DFNA40) [MIM:616357]: A form of non-syndromic sensorineural hearing loss. Sensorineural deafness results from damage to the neural receptors of the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information. {ECO:0000269 PubMed:12471561}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for CRYM

genes like me logo Genes that share disorders with CRYM: view

No data available for Genatlas for CRYM Gene

Publications for CRYM Gene

  1. Mammalian forebrain ketimine reductase identified as μ-crystallin; potential regulation by thyroid hormones. (PMID: 21332720) Hallen A … Willows RD (Journal of neurochemistry 2011) 2 3 4 58
  2. Crystal structure of human micro-crystallin complexed with NADPH. (PMID: 17242435) Cheng Z … Gong W (Protein science : a publication of the Protein Society 2007) 3 4 22 58
  3. Identification of CRYM as a candidate responsible for nonsyndromic deafness, through cDNA microarray analysis of human cochlear and vestibular tissues. (PMID: 12471561) Abe S … Nakamura Y (American journal of human genetics 2003) 3 4 22 58
  4. Two roles for mu-crystallin: a lens structural protein in diurnal marsupials and a possible enzyme in mammalian retinas. (PMID: 9285773) Segovia L … Wistow G (Molecular vision 1997) 3 4 22 58
  5. Purification, molecular cloning, and functional expression of the human nicodinamide-adenine dinucleotide phosphate-regulated thyroid hormone-binding protein. (PMID: 9328354) Vié MP … Blondeau JP (Molecular endocrinology (Baltimore, Md.) 1997) 3 4 22 58

Products for CRYM Gene

Sources for CRYM Gene

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