This gene encodes a protein with high similarity to the calcium-binding proteins of the calmodulin family. The encoded protein contains two EF-hand domains and potential calcium-binding sites. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2008] See more...

Aliases for CALN1 Gene

Aliases for CALN1 Gene

  • Calneuron 1 2 3 5
  • CABP8 2 3 4
  • Calcium-Binding Protein CABP8 2 3
  • Calcium-Binding Protein 8 3 4
  • Calneuron I 3 4
  • Calneuron-1 4
  • CALN1 5
  • CaBP8 4

External Ids for CALN1 Gene

Previous GeneCards Identifiers for CALN1 Gene

  • GC07M069888
  • GC07M070646
  • GC07M070660
  • GC07M070692
  • GC07M070885
  • GC07M071244
  • GC07M067413

Summaries for CALN1 Gene

Entrez Gene Summary for CALN1 Gene

  • This gene encodes a protein with high similarity to the calcium-binding proteins of the calmodulin family. The encoded protein contains two EF-hand domains and potential calcium-binding sites. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2008]

GeneCards Summary for CALN1 Gene

CALN1 (Calneuron 1) is a Protein Coding gene. Diseases associated with CALN1 include Deafness, Autosomal Recessive 39 and D-Glyceric Aciduria. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is CABP7.

UniProtKB/Swiss-Prot Summary for CALN1 Gene

  • Negatively regulates Golgi-to-plasma membrane trafficking by interacting with PI4KB and inhibiting its activity (By similarity). May play a role in the physiology of neurons and is potentially important in memory and learning.

Gene Wiki entry for CALN1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CALN1 Gene

Genomics for CALN1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CALN1 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
GH07J072337 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 600.1 +167.7 167742 2.7 CTCF POLR2A EZH2 RAD21 TAF1 EGR1 CALN1 GTF2IP4 RF00017-6289 piR-57460-622 RF00017-6287
GH07J072412 Promoter 0.8 EPDnew 611.7 +91.9 91913 0.1 POLR2A MTA3 TAF9B ZNF316 MAFG TBP SMAD5 SUPT5H NFATC3 FOS CALN1 piR-54465 RF00017-6290
GH07J072447 Promoter 0.4 EPDnew 600.2 +57.1 57113 0.1 ZFP91 CALN1 RF00017-6290 piR-54465
GH07J072503 Enhancer 0.4 Ensembl 600.7 +0.3 270 0.4 TFAP4 HLF CEBPB CALN1 NSUN5P2 RF00017-6291
GH07J072403 Enhancer 1.1 FANTOM5 Ensembl ENCODE 11.7 +100.2 100170 5 CREB1 JUND ZSCAN4 PKNOX1 EED CEBPB RFX1 HMBOX1 RELB EGR1 CALN1 TYW1B FKBP6 piR-54465 piR-57460-622
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CALN1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CALN1

Top Transcription factor binding sites by QIAGEN in the CALN1 gene promoter:
  • HOXA9
  • HOXA9B
  • Meis-1
  • Meis-1b
  • p300
  • Pax-4a
  • POU2F1
  • POU2F1a
  • YY1

Genomic Locations for CALN1 Gene

Genomic Locations for CALN1 Gene
chr7:71,779,491-72,504,271
(GRCh38/hg38)
Size:
724,781 bases
Orientation:
Minus strand
chr7:71,244,476-71,912,136
(GRCh37/hg19)
Size:
667,661 bases
Orientation:
Minus strand

Genomic View for CALN1 Gene

Genes around CALN1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CALN1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CALN1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CALN1 Gene

Proteins for CALN1 Gene

  • Protein details for CALN1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BXU9-CABP8_HUMAN
    Recommended name:
    Calcium-binding protein 8
    Protein Accession:
    Q9BXU9
    Secondary Accessions:
    • J3KQA7

    Protein attributes for CALN1 Gene

    Size:
    219 amino acids
    Molecular mass:
    24837 Da
    Quaternary structure:
    • Interacts with PI4KB. This binding competes with FREQ/NCS1 binding in a calcium-dependent manner (By similarity).
    SequenceCaution:
    • Sequence=AAG09620.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};

    Alternative splice isoforms for CALN1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CALN1 Gene

Post-translational modifications for CALN1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for CALN1 Gene

Domains & Families for CALN1 Gene

Gene Families for CALN1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for CALN1 Gene

Suggested Antigen Peptide Sequences for CALN1 Gene

GenScript: Design optimal peptide antigens:
  • cDNA, FLJ93531, Homo sapiens calneuron 1 (CALN1), mRNA (A4D1Z1_HUMAN)
  • Calneuron-1 (CABP8_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9BXU9

UniProtKB/Swiss-Prot:

CABP8_HUMAN :
  • The C-terminal transmembrane domain (TMD) is necessary and sufficient for membrane targeting.
Domain:
  • The C-terminal transmembrane domain (TMD) is necessary and sufficient for membrane targeting.
genes like me logo Genes that share domains with CALN1: view

Function for CALN1 Gene

Molecular function for CALN1 Gene

UniProtKB/Swiss-Prot Function:
Negatively regulates Golgi-to-plasma membrane trafficking by interacting with PI4KB and inhibiting its activity (By similarity). May play a role in the physiology of neurons and is potentially important in memory and learning.

Phenotypes From GWAS Catalog for CALN1 Gene

Gene Ontology (GO) - Molecular Function for CALN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
GO:0005515 protein binding IPI 30073165
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with CALN1: view
genes like me logo Genes that share phenotypes with CALN1: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CALN1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CALN1 Gene

Localization for CALN1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CALN1 Gene

Golgi apparatus, trans-Golgi network membrane. Single-pass type IV membrane protein. Cytoplasm, perinuclear region. Cell membrane. Single-pass type IV membrane protein.

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 CALN1 gene
Compartment Confidence
golgi apparatus 5
plasma membrane 4
cytosol 3
nucleus 2
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Plasma membrane (1)
  • Vesicles (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CALN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005794 Golgi apparatus IEA --
GO:0005886 plasma membrane IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with CALN1: view

Pathways & Interactions for CALN1 Gene

PathCards logo

SuperPathways for CALN1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for CALN1 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for CALN1 Gene

Drugs & Compounds for CALN1 Gene

No Compound Related Data Available

Transcripts for CALN1 Gene

mRNA/cDNA for CALN1 Gene

3 REFSEQ mRNAs :
14 NCBI additional mRNA sequence :
6 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CALN1

Alternative Splicing Database (ASD) splice patterns (SP) for CALN1 Gene

No ASD Table

Relevant External Links for CALN1 Gene

GeneLoc Exon Structure for
CALN1

Expression for CALN1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CALN1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CALN1 Gene

This gene is overexpressed in Brain - Cerebellar Hemisphere (x11.1), Brain - Cerebellum (x8.5), and Brain - Nucleus accumbens (basal ganglia) (x4.4).

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CALN1

SOURCE GeneReport for Unigene cluster for CALN1 Gene:

Hs.592750

mRNA Expression by UniProt/SwissProt for CALN1 Gene:

Q9BXU9-CABP8_HUMAN
Tissue specificity: Brain specific.

Evidence on tissue expression from TISSUES for CALN1 Gene

  • Nervous system(5)
  • Eye(4.6)
  • Lung(4.6)
  • Intestine(2.5)
  • Liver(2.5)
  • Skin(2.2)
  • Kidney(2.1)
genes like me logo Genes that share expression patterns with CALN1: view

No data available for Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for CALN1 Gene

Orthologs for CALN1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CALN1 Gene

Organism Taxonomy Gene Similarity Type Details
Platypus
(Ornithorhynchus anatinus)
Mammalia CALN1 31
  • 100 (a)
OneToOne
Chimpanzee
(Pan troglodytes)
Mammalia CALN1 30 31
  • 99.49 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia CALN1 31
  • 95 (a)
OneToOne
Cow
(Bos Taurus)
Mammalia CALN1 30 31
  • 93.23 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia CALN1 30 31
  • 91.32 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Caln1 30 17 31
  • 89.27 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Caln1 30
  • 88.25 (n)
Chicken
(Gallus gallus)
Aves CALN1 30 31
  • 84.97 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia CALN1 31
  • 99 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia caln1 30
  • 79.45 (n)
Zebrafish
(Danio rerio)
Actinopterygii caln2 31
  • 88 (a)
OneToMany
LOC562420 30
  • 80.56 (n)
CALN1 (2 of 2) 31
  • 80 (a)
OneToMany
Species where no ortholog for CALN1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • 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)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • 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 (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for CALN1 Gene

ENSEMBL:
Gene Tree for CALN1 (if available)
TreeFam:
Gene Tree for CALN1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CALN1: view image

Paralogs for CALN1 Gene

(11) SIMAP similar genes for CALN1 Gene using alignment to 9 proteins:

  • CABP8_HUMAN
  • A4D1Z1_HUMAN
  • E9PFU3_HUMAN
  • L8ECK9_HUMAN
  • Q75MI2_HUMAN
  • Q75MP5_HUMAN
  • Q75MW5_HUMAN
  • Q86UL5_HUMAN
  • Q86UM7_HUMAN
genes like me logo Genes that share paralogs with CALN1: view

Variants for CALN1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CALN1 Gene

SNP ID Clinical significance and condition Chr 07 pos Variation AA Info Type
714347 Benign: not provided 72,106,206(-) C/T SYNONYMOUS_VARIANT
774654 Benign: not provided 71,810,328(-) G/T INTRON_VARIANT

Additional dbSNP identifiers (rs#s) for CALN1 Gene

Structural Variations from Database of Genomic Variants (DGV) for CALN1 Gene

Variant ID Type Subtype PubMed ID
dgv150e203 CNV loss 21179565
dgv6456n100 CNV gain 25217958
dgv6457n100 CNV loss 25217958
dgv6458n100 CNV loss 25217958
esv1045517 CNV deletion 17803354
esv24358 CNV loss 19812545
esv2660292 CNV deletion 23128226
esv2662393 CNV deletion 23128226
esv2664115 CNV deletion 23128226
esv2671768 CNV deletion 23128226
esv2676220 CNV deletion 23128226
esv2761106 CNV gain 21179565
esv3342742 CNV insertion 20981092
esv3439105 CNV insertion 20981092
esv3442412 CNV insertion 20981092
esv3541884 CNV deletion 23714750
esv3541887 CNV deletion 23714750
esv3541890 CNV deletion 23714750
esv3571915 CNV loss 25503493
esv3571916 CNV loss 25503493
esv3613640 CNV gain 21293372
esv3613641 CNV loss 21293372
esv3613643 CNV loss 21293372
esv3613646 CNV loss 21293372
esv3613648 CNV loss 21293372
esv3613649 CNV loss 21293372
esv3613650 CNV loss 21293372
esv3613651 CNV loss 21293372
esv3613652 CNV loss 21293372
esv3613653 CNV loss 21293372
esv3613654 CNV loss 21293372
esv3613655 CNV loss 21293372
esv3613656 CNV loss 21293372
esv3613657 CNV loss 21293372
esv3613658 CNV loss 21293372
esv3891142 CNV loss 25118596
esv3891143 CNV loss 25118596
nsv1017575 CNV gain 25217958
nsv1023496 CNV gain 25217958
nsv1026896 CNV gain 25217958
nsv1033922 CNV gain 25217958
nsv1146102 OTHER inversion 26484159
nsv428170 CNV loss 18775914
nsv464556 CNV loss 19166990
nsv470299 CNV loss 18288195
nsv477276 CNV novel sequence insertion 20440878
nsv516049 CNV gain 19592680
nsv517305 CNV loss 19592680
nsv524800 CNV loss 19592680
nsv527501 CNV loss 19592680
nsv528974 CNV loss 19592680
nsv607459 CNV gain 21841781
nsv607460 CNV loss 21841781
nsv607461 CNV loss 21841781
nsv831023 CNV loss 17160897
nsv831024 CNV loss 17160897
nsv957627 CNV deletion 24416366

Variation tolerance for CALN1 Gene

Residual Variation Intolerance Score: 30.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.76; 16.05% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CALN1 Gene

Human Gene Mutation Database (HGMD)
CALN1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CALN1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CALN1 Gene

Disorders for CALN1 Gene

MalaCards: The human disease database

(4) MalaCards diseases for CALN1 Gene - From: DISEASES

Disorder Aliases PubMed IDs
deafness, autosomal recessive 39
  • dfnb39
d-glyceric aciduria
  • d-glyceric acidemia
drug psychosis
  • drug-induced psychosis
drug-induced mental disorder
- elite association - COSMIC cancer census association via MalaCards
Search CALN1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CALN1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with CALN1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CALN1 Gene

Publications for CALN1 Gene

  1. Identification of a human brain-specific gene, calneuron 1, a new member of the calmodulin superfamily. (PMID: 11286509) Wu YQ … Shaffer LG (Molecular genetics and metabolism 2001) 2 3 4 23
  2. Genome-wide association study identifies five new schizophrenia loci. (PMID: 21926974) Schizophrenia Psychiatric Genome-Wide Association Study (GWAS) Consortium (Nature genetics 2011) 3 41
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41
  4. Membrane targeting of the EF-hand containing calcium-sensing proteins CaBP7 and CaBP8. (PMID: 19338761) McCue HV … Haynes LP (Biochemical and biophysical research communications 2009) 3 4
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4

Products for CALN1 Gene

Sources for CALN1 Gene