This gene encodes a member of the neuronal calcium sensor (NCS) family of calcium-binding proteins. The protein contains an N-terminal myristoylation signal and four EF-hand calcium binding loops. The protein is cytosolic at resting calcium levels; however, elevated intracellular calcium levels induce a conformational change that exposes the myristoyl group, resulting in protei... See more...

Aliases for NCALD Gene

Aliases for NCALD Gene

  • Neurocalcin Delta 2 3 5
  • Neurocalcin-Delta 3 4
  • NCALD 5

External Ids for NCALD Gene

Previous GeneCards Identifiers for NCALD Gene

  • GC08M102766
  • GC08M102367
  • GC08M102655
  • GC08M102767
  • GC08M097897
  • GC08M102698

Summaries for NCALD Gene

Entrez Gene Summary for NCALD Gene

  • This gene encodes a member of the neuronal calcium sensor (NCS) family of calcium-binding proteins. The protein contains an N-terminal myristoylation signal and four EF-hand calcium binding loops. The protein is cytosolic at resting calcium levels; however, elevated intracellular calcium levels induce a conformational change that exposes the myristoyl group, resulting in protein association with membranes and partial co-localization with the perinuclear trans-golgi network. The protein is thought to be a regulator of G protein-coupled receptor signal transduction. Several alternatively spliced variants of this gene have been determined, all of which encode the same protein; additional variants may exist but their biological validity has not been determined. [provided by RefSeq, Jul 2008]

GeneCards Summary for NCALD Gene

NCALD (Neurocalcin Delta) is a Protein Coding gene. Diseases associated with NCALD include Spinal Muscular Atrophy, Type Iv and Spinal Muscular Atrophy. Among its related pathways are Transmission across Chemical Synapses and Presynaptic function of Kainate receptors. Gene Ontology (GO) annotations related to this gene include calcium ion binding and clathrin binding. An important paralog of this gene is HPCAL1.

UniProtKB/Swiss-Prot Summary for NCALD Gene

  • May be involved in the calcium-dependent regulation of rhodopsin phosphorylation. Binds three calcium ions.

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

Genomics for NCALD Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for NCALD 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
GH08J102120 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 609.5 +2.0 2008 4.2 CTCF ZNF143 PATZ1 IKZF2 RCOR1 POLR2A SIN3A RAD21 DPF2 ZNF524 NCALD 5EW4_A-046 lnc-RRM2B-8 UBR5 LOC104054148 GRHL2
GH08J101789 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 600.1 +334.8 334807 3.3 CREB1 ZNF629 REST RFX1 POLR2A SP1 PKNOX1 ZBTB44 ZSCAN29 RAD21 lnc-RRM2B-7 NCALD ENSG00000253629 piR-35031-043 GRHL2 lnc-RRM2B-8
GH08J102199 Promoter 0.6 EPDnew 600.2 -74.4 -74449 0.1 ELF1 SP1 GABPB1 POLR2A NCALD RF00017-7236 HSALNG0067413 RRM2B
GH08J102094 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 20 +28.2 28203 4.6 BACH1 LARP7 ZNF143 RELA TCF12 IKZF2 TRIM22 YY1 PKNOX1 ATF7 NCALD ZNF706 UBR5 5EW4_A-046 lnc-RRM2B-8 LOC104054148 GRHL2
GH08J101967 Enhancer 0.9 Ensembl ENCODE 15.2 +157.0 156997 1.8 POLR2A FOXA1 SP1 TRIM22 PKNOX1 RUNX3 CTBP1 FOXA2 ZNF444 YY1 NCALD LOC107986963 LOC104054148 lnc-RRM2B-8 GRHL2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

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

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

Top Transcription factor binding sites by QIAGEN in the NCALD gene promoter:
  • AML1a
  • ATF-2
  • FOXO3
  • FOXO3a
  • FOXO3b
  • HOXA3

Genomic Locations for NCALD Gene

Genomic Locations for NCALD Gene
chr8:101,686,542-102,125,081
(GRCh38/hg38)
Size:
438,540 bases
Orientation:
Minus strand
chr8:102,698,770-103,137,135
(GRCh37/hg19)
Size:
438,366 bases
Orientation:
Minus strand

Genomic View for NCALD Gene

Genes around NCALD on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for NCALD Gene

Proteins for NCALD Gene

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

    Protein Symbol:
    P61601-NCALD_HUMAN
    Recommended name:
    Neurocalcin-delta
    Protein Accession:
    P61601
    Secondary Accessions:
    • P29554
    • Q8IYC3
    • Q9H0W2

    Protein attributes for NCALD Gene

    Size:
    193 amino acids
    Molecular mass:
    22245 Da
    Quaternary structure:
    • Interacts with GUCY2D.

neXtProt entry for NCALD Gene

Post-translational modifications for NCALD Gene

  • Ubiquitination at Lys50
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for NCALD Gene

Domains & Families for NCALD Gene

Gene Families for NCALD Gene

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

Protein Domains for NCALD Gene

InterPro:
Blocks:
  • Recoverin family signature
ProtoNet:

Suggested Antigen Peptide Sequences for NCALD Gene

GenScript: Design optimal peptide antigens:
  • cDNA, FLJ95342, highly similar to Homo sapiens neurocalcin delta (NCALD), mRNA (B2RB70_HUMAN)
  • Neurocalcin-delta (NCALD_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P61601

UniProtKB/Swiss-Prot:

NCALD_HUMAN :
  • Belongs to the recoverin family.
Family:
  • Belongs to the recoverin family.
genes like me logo Genes that share domains with NCALD: view

Function for NCALD Gene

Molecular function for NCALD Gene

UniProtKB/Swiss-Prot Function:
May be involved in the calcium-dependent regulation of rhodopsin phosphorylation. Binds three calcium ions.

Phenotypes From GWAS Catalog for NCALD Gene

Gene Ontology (GO) - Molecular Function for NCALD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003779 actin binding IDA 11964161
GO:0005509 calcium ion binding IEA --
GO:0005515 protein binding IPI 16189514
GO:0015631 tubulin binding IDA 11964161
GO:0030276 clathrin binding IDA 11964161
genes like me logo Genes that share ontologies with NCALD: view
genes like me logo Genes that share phenotypes with NCALD: view

Animal Models for NCALD Gene

MGI Knock Outs for NCALD:
  • Ncald Ncald<tm1.1(KOMP)Vlcg>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

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

Clone Products

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

Localization for NCALD Gene

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 NCALD gene
Compartment Confidence
cytosol 5
golgi apparatus 5
nucleus 3
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for NCALD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IDA --
GO:0005829 cytosol TAS --
GO:0030130 clathrin coat of trans-Golgi network vesicle NAS 11964161
genes like me logo Genes that share ontologies with NCALD: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Subcellular locations from the Human Protein Atlas (HPA) for NCALD Gene

Pathways & Interactions for NCALD Gene

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

Gene Ontology (GO) - Biological Process for NCALD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003073 regulation of systemic arterial blood pressure IEA --
GO:0016192 vesicle-mediated transport NAS 11964161
GO:0019722 calcium-mediated signaling IEA --
genes like me logo Genes that share ontologies with NCALD: view

No data available for SIGNOR curated interactions for NCALD Gene

Drugs & Compounds for NCALD Gene

(1) Drugs for NCALD Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Calcium Nutra 6556
genes like me logo Genes that share compounds with NCALD: view

Transcripts for NCALD Gene

mRNA/cDNA for NCALD Gene

8 REFSEQ mRNAs :
21 NCBI additional mRNA sequence :
30 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 NCALD

Clone Products

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

ExUns: 1a · 1b ^ 2a · 2b · 2c ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17a · 17b · 17c ^ 18 ^ 19 ^ 20 ^
SP1: - - -
SP2: - - - - - - - - - - - - - - - - - -
SP3: - - - - - - - - - - - - - - - -
SP4: - - - - - - - - - - - - - - -
SP5: - - - - - - - - - - - - - - - - - - -
SP6: - - - - - - - - - - - - - - - -
SP7: - - - - - - - - - - - - - -
SP8: - - - - - - - - - - - - - -
SP9: - - - - - - -
SP10: - - -
SP11: - - -
SP12: - - - - - - - - - - - - - - - - - -
SP13: - - - - - - - - - - - - - - -
SP14: - - - - - - - - - - - - - - - -
SP15: - - - - - - - - - - - - - - - - - - - - - - -
SP16: - - - - - - - - - - - - - - - - - - - - -
SP17: - -
SP18: -
SP19: - -
SP20:
SP21:

ExUns: 21a · 21b ^ 22a · 22b · 22c · 22d · 22e · 22f ^ 23 ^ 24a · 24b · 24c ^ 25 ^ 26
SP1:
SP2: - -
SP3: - -
SP4:
SP5: -
SP6:
SP7:
SP8: -
SP9: - -
SP10: - -
SP11: -
SP12: -
SP13:
SP14:
SP15:
SP16: -
SP17:
SP18:
SP19:
SP20: -
SP21:

Relevant External Links for NCALD Gene

GeneLoc Exon Structure for
NCALD

Expression for NCALD Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

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

This gene is overexpressed in Brain - Cortex (x7.8), Brain - Frontal Cortex (BA9) (x7.3), and Brain - Anterior cingulate cortex (BA24) (x4.5).

Protein differential expression in normal tissues from HIPED for NCALD Gene

This gene is overexpressed in Frontal cortex (26.4), Salivary gland (11.7), and Brain (7.3).

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



Protein tissue co-expression partners for NCALD Gene

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

SOURCE GeneReport for Unigene cluster for NCALD Gene:

Hs.492427

mRNA Expression by UniProt/SwissProt for NCALD Gene:

P61601-NCALD_HUMAN
Tissue specificity: Retina, cerebrum, cerebellum, brain stem, spinal cord, testis, ovary and small intestine.

Evidence on tissue expression from TISSUES for NCALD Gene

  • Nervous system(5)
  • Eye(2.3)
  • Lung(2.2)
  • Kidney(2.1)
genes like me logo Genes that share expression patterns with NCALD: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for NCALD Gene

Orthologs for NCALD Gene

This gene was present in the common ancestor of animals.

Orthologs for NCALD Gene

Organism Taxonomy Gene Similarity Type Details
Oppossum
(Monodelphis domestica)
Mammalia NCALD 31
  • 100 (a)
OneToOne
Chimpanzee
(Pan troglodytes)
Mammalia NCALD 30 31
  • 99.48 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia NCALD 30 31
  • 95.34 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Ncald 30
  • 93.09 (n)
Cow
(Bos Taurus)
Mammalia NCALD 30 31
  • 93.09 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Ncald 30 17 31
  • 92.57 (n)
OneToOne
Chicken
(Gallus gallus)
Aves NCALD 30 31
  • 86.36 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia NCALD 31
  • 100 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia ncald 30
  • 84.11 (n)
Str.14728 30
Zebrafish
(Danio rerio)
Actinopterygii ncaldb 31
  • 94 (a)
OneToMany
ncalda 30 31
  • 81.35 (n)
OneToMany
Fruit Fly
(Drosophila melanogaster)
Insecta Nca 32
  • 87 (a)
CG7646 32
  • 47 (a)
Worm
(Caenorhabditis elegans)
Secernentea ncs-3 32
  • 58 (a)
ncs-2 32
  • 50 (a)
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 77 (a)
OneToMany
Species where no ortholog for NCALD 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)
  • 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)
  • Platypus (Ornithorhynchus anatinus)
  • 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 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)

Evolution for NCALD Gene

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

Paralogs for NCALD Gene

(24) SIMAP similar genes for NCALD Gene using alignment to 18 proteins:

  • NCALD_HUMAN
  • B2RB70_HUMAN
  • E5RFL9_HUMAN
  • E5RGA9_HUMAN
  • E5RGZ0_HUMAN
  • E5RHC8_HUMAN
  • E5RHE8_HUMAN
  • E5RI78_HUMAN
  • E5RI95_HUMAN
  • E5RIA5_HUMAN
  • E5RIG4_HUMAN
  • E5RIX3_HUMAN
  • E5RIZ1_HUMAN
  • E5RJA1_HUMAN
  • E5RJF1_HUMAN
  • E5RJJ6_HUMAN
  • E5RJT1_HUMAN
  • E5RK89_HUMAN
genes like me logo Genes that share paralogs with NCALD: view

Variants for NCALD Gene

Additional dbSNP identifiers (rs#s) for NCALD Gene

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

Variant ID Type Subtype PubMed ID
dgv466n21 CNV loss 19592680
esv21888 CNV loss 19812545
esv2421949 CNV deletion 20811451
esv2605083 CNV insertion 19546169
esv2662515 CNV deletion 23128226
esv2664408 CNV deletion 23128226
esv2737371 CNV deletion 23290073
esv2761453 CNV loss 21179565
esv3310355 CNV mobile element insertion 20981092
esv3431444 CNV duplication 20981092
esv3448877 CNV insertion 20981092
esv3543934 CNV deletion 23714750
esv3618213 CNV loss 21293372
esv3618214 CNV loss 21293372
esv3618216 CNV loss 21293372
esv3618217 CNV loss 21293372
esv3891452 CNV loss 25118596
nsv1020359 CNV gain 25217958
nsv1030076 CNV loss 25217958
nsv1076099 CNV deletion 25765185
nsv1137618 CNV deletion 24896259
nsv1139941 CNV duplication 24896259
nsv1152951 CNV deletion 26484159
nsv438074 CNV loss 16468122
nsv465749 CNV loss 19166990
nsv507478 OTHER sequence alteration 20534489
nsv517149 CNV loss 19592680
nsv517893 CNV loss 19592680
nsv523654 CNV gain 19592680
nsv611819 CNV loss 21841781
nsv611820 CNV loss 21841781
nsv818646 CNV loss 17921354
nsv831411 CNV gain 17160897
nsv8371 CNV loss 18304495
nsv981971 CNV duplication 23825009

Variation tolerance for NCALD Gene

Residual Variation Intolerance Score: 37.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.50; 10.82% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NCALD Gene

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

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for NCALD Gene

Disorders for NCALD Gene

MalaCards: The human disease database

(6) MalaCards diseases for NCALD Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
spinal muscular atrophy, type iv
  • sma4
spinal muscular atrophy
  • progressive muscular atrophy
leber congenital amaurosis 1
  • lca1
spinal muscular atrophy, type ii
  • sma2
childhood spinal muscular atrophy
  • spinal muscular atrophies of childhood
- elite association - COSMIC cancer census association via MalaCards
Search NCALD in MalaCards View complete list of genes associated with diseases

Additional Disease Information for NCALD

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 NCALD: view

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

Publications for NCALD Gene

  1. Molecular cloning, mapping and characterization of the human neurocalcin delta gene (NCALD). (PMID: 11267673) Wang W … Mao Y (Biochimica et biophysica acta 2001) 2 3 4 23
  2. Polymorphisms in the 3' UTR in the neurocalcin delta gene affect mRNA stability, and confer susceptibility to diabetic nephropathy. (PMID: 17671797) Kamiyama M … Maeda S (Human genetics 2007) 3 23 41
  3. Genome-wide association analysis of coffee drinking suggests association with CYP1A1/CYP1A2 and NRCAM. (PMID: 21876539) Amin N … van Duijn CM (Molecular psychiatry 2012) 3 41
  4. 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
  5. Common genetic variation and performance on standardized cognitive tests. (PMID: 20125193) Cirulli ET … Goldstein DB (European journal of human genetics : EJHG 2010) 3 41

Products for NCALD Gene

Sources for NCALD Gene