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    NCALD neurocalcin delta [ Homo sapiens (human) ]

    Gene ID: 83988, updated on 10-Dec-2024

    Summary

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    Official Symbol
    NCALDprovided by HGNC
    Official Full Name
    neurocalcin deltaprovided by HGNC
    Primary source
    HGNC:HGNC:7655
    See related
    Ensembl:ENSG00000104490 MIM:606722; AllianceGenome:HGNC:7655
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    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]
    Expression
    Broad expression in brain (RPKM 22.6), salivary gland (RPKM 11.3) and 20 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See NCALD in Genome Data Viewer
    Location:
    8q22.3
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (101686542..102124907, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (102812429..103250775, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (102698770..103137135, complement)

    Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene SAP domain containing ribonucleoprotein pseudogene Neighboring gene grainyhead like transcription factor 2 Neighboring gene probable ribosome biogenesis protein RLP24 Neighboring gene Sharpr-MPRA regulatory region 9664 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr8:102655529-102656728 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:102659137-102659637 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:102668311-102669171 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27732 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27733 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr8:102762302-102763501 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27734 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27735 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:102799260-102799806 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:102799807-102800353 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27736 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19433 Neighboring gene small nucleolar RNA U13 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:102903930-102904473 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27738 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27737 Neighboring gene uncharacterized LOC124901996 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27739 Neighboring gene PDCL3 pseudogene 2 Neighboring gene NANOG hESC enhancer GRCh37_chr8:102948047-102948548 Neighboring gene uncharacterized LOC104054148 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27740 Neighboring gene uncharacterized LOC124901997 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr8:103078318-103078896 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_100837 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27741 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27742 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27743 Neighboring gene NANOG hESC enhancer GRCh37_chr8:103124713-103125214 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19434 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19435 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:103144879-103145380 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:103145381-103145880 Neighboring gene ATP synthase subunit ATP5MJ, mitochondrial-like Neighboring gene microRNA 5680

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Molecular cloning, mapping and characterization of the human neurocalcin delta gene (NCALD). Wang W, et al. Biochim Biophys Acta, 2001 Mar 19. PMID 11267673
    2. Polymorphisms in the 3' UTR in the neurocalcin delta gene affect mRNA stability, and confer susceptibility to diabetic nephropathy. Kamiyama M, et al. Hum Genet, 2007 Nov. PMID 17671797
    3. Low expression of NCALD is associated with chemotherapy resistance and poor prognosis in epithelial ovarian cancer. Feng LY, et al. J Ovarian Res, 2020 Mar 30. PMID 32228639, Free PMC Article
    4. NCALD affects drug resistance and prognosis by acting as a ceRNA of CX3CL1 in ovarian cancer. Dong C, et al. J Cell Biochem, 2020 Nov. PMID 32030795
    5. High NCALD expression predicts poor prognosis of cytogenetic normal acute myeloid leukemia. Song Y, et al. J Transl Med, 2019 May 20. PMID 31109331, Free PMC Article

    See all (46) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. NCALD affects drug resistance and prognosis by acting as a ceRNA of CX3CL1 in ovarian cancer.
      Title: NCALD affects drug resistance and prognosis by acting as a ceRNA of CX3CL1 in ovarian cancer.
    2. Low expression of NCALD is associated with chemotherapy resistance and poor prognosis in epithelial ovarian cancer.
      Title: Low expression of NCALD is associated with chemotherapy resistance and poor prognosis in epithelial ovarian cancer.
    3. high expression of NCALD gene is a poor prognostic factor for cytogenetic normal acute myeloid leukemia.
      Title: High NCALD expression predicts poor prognosis of cytogenetic normal acute myeloid leukemia.
    4. Coffee consumption is causally associated with an increased risk of osteoarthritis. SNPs in NCALD, POR, CYP1A1 and NRCAM were identified.
      Title: Investigating the possible causal association of coffee consumption with osteoarthritis risk using a Mendelian randomization analysis.
    5. Neurocalcin delta is a protective spinal muscular atrophy modifier in five asymptomatic SMN1-deleted individuals carrying only four SMN2 copies.
      Title: Neurocalcin Delta Suppression Protects against Spinal Muscular Atrophy in Humans and across Species by Restoring Impaired Endocytosis.
    6. It is presumed that NCALD is related to diabetic nephropathy by promoting epithelial mesenchymal transform.
      Title: [Genetic study for diabetic microvascular complications--recent advances and future perspectives].
    7. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    8. Studies show that a fold recognition based model of the catalytic domain of ROS-GC1 was built, and neurocalcin delta docking simulations were carried out to define the three-dimensional features of the interacting domains of the two molecules.
      Title: Neurocalcin delta modulation of ROS-GC1, a new model of Ca(2+) signaling.
    9. association of the landmark SNP with the progression of diabetic nephropathy in a 8-year prospective study
      Title: Polymorphisms in the 3' UTR in the neurocalcin delta gene affect mRNA stability, and confer susceptibility to diabetic nephropathy.
    10. Observational study of gene-disease association. (HuGE Navigator)
      Title: Polymorphisms in the 3' UTR in the neurocalcin delta gene affect mRNA stability, and confer susceptibility to diabetic nephropathy.
    Submit: New GeneRIF Correction See all GeneRIFs (11)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Common genetic variation and performance on standardized cognitive tests.
    EBI GWAS Catalog
    Genome-wide association analysis demonstrates the highly polygenic character of age-related hearing impairment.
    EBI GWAS Catalog
    Genome-wide association analysis of coffee drinking suggests association with CYP1A1/CYP1A2 and NRCAM.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC33870, MGC74858

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables actin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables actin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables alpha-tubulin binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables calcium ion binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables clathrin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables tubulin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables tubulin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in calcium-mediated signaling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of systemic arterial blood pressure IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in vesicle-mediated transport NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of clathrin coat of trans-Golgi network vesicle NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in cytosol NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    neurocalcin-delta

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001040624.2 → NP_001035714.1  neurocalcin-delta

      See identical proteins and their annotated locations for NP_001035714.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) includes five untranslated exons at the 5' end.
      Source sequence(s)
      AP000426, AP001206, AP001328, AP001575
      Consensus CDS
      CCDS6292.1
      UniProtKB/Swiss-Prot
      P29554, P61601, Q8IYC3, Q9H0W2
      UniProtKB/TrEMBL
      B2RB70, E5RGA9
      Conserved Domains (1) summary
      COG5126
      Location:14 → 179
      FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]

    2. NM_001040625.2 → NP_001035715.1  neurocalcin-delta

      See identical proteins and their annotated locations for NP_001035715.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an exon in the 5' UTR compared to variant 1.
      Source sequence(s)
      AP000426, BC063428, BM681731
      Consensus CDS
      CCDS6292.1
      UniProtKB/Swiss-Prot
      P29554, P61601, Q8IYC3, Q9H0W2
      UniProtKB/TrEMBL
      B2RB70, E5RGA9
      Related
      ENSP00000428105.1, ENST00000521599.5
      Conserved Domains (1) summary
      COG5126
      Location:14 → 179
      FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]

    3. NM_001040626.2 → NP_001035716.1  neurocalcin-delta

      See identical proteins and their annotated locations for NP_001035716.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an exon in the 5' UTR compared to variant 1.
      Source sequence(s)
      AP000426, AP001206, AP001328, AP001575
      Consensus CDS
      CCDS6292.1
      UniProtKB/Swiss-Prot
      P29554, P61601, Q8IYC3, Q9H0W2
      UniProtKB/TrEMBL
      B2RB70, E5RGA9
      Related
      ENSP00000310587.3, ENST00000311028.4
      Conserved Domains (1) summary
      COG5126
      Location:14 → 179
      FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]

    4. NM_001040627.2 → NP_001035717.1  neurocalcin-delta

      See identical proteins and their annotated locations for NP_001035717.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks two exons in the 5' UTR compared to variant 1.
      Source sequence(s)
      AP000426, BC036098, BC063428, BM681731, DA417037
      Consensus CDS
      CCDS6292.1
      UniProtKB/Swiss-Prot
      P29554, P61601, Q8IYC3, Q9H0W2
      UniProtKB/TrEMBL
      B2RB70, E5RGA9
      Conserved Domains (1) summary
      COG5126
      Location:14 → 179
      FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]

    5. NM_001040628.2 → NP_001035718.1  neurocalcin-delta

      See identical proteins and their annotated locations for NP_001035718.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR compared to variant 1.
      Source sequence(s)
      AP000426, BC063428, BM681731, DA417037, DA776593
      Consensus CDS
      CCDS6292.1
      UniProtKB/Swiss-Prot
      P29554, P61601, Q8IYC3, Q9H0W2
      UniProtKB/TrEMBL
      B2RB70, E5RGA9
      Conserved Domains (1) summary
      COG5126
      Location:14 → 179
      FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]

    6. NM_001040629.2 → NP_001035719.1  neurocalcin-delta

      See identical proteins and their annotated locations for NP_001035719.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) differs in the 5' UTR compared to variant 1.
      Source sequence(s)
      AP000426, BC063428, BM681731, DA417037, DA779293
      Consensus CDS
      CCDS6292.1
      UniProtKB/Swiss-Prot
      P29554, P61601, Q8IYC3, Q9H0W2
      UniProtKB/TrEMBL
      B2RB70, E5RGA9
      Conserved Domains (1) summary
      COG5126
      Location:14 → 179
      FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]

    7. NM_001040630.2 → NP_001035720.1  neurocalcin-delta

      See identical proteins and their annotated locations for NP_001035720.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) differs in the 5' UTR compared to variant 1.
      Source sequence(s)
      AP000426, BC063428, BM681731, DA215759, DB284042
      Consensus CDS
      CCDS6292.1
      UniProtKB/Swiss-Prot
      P29554, P61601, Q8IYC3, Q9H0W2
      UniProtKB/TrEMBL
      B2RB70, E5RGA9
      Related
      ENSP00000379256.1, ENST00000395923.5
      Conserved Domains (1) summary
      COG5126
      Location:14 → 179
      FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]

    8. NM_032041.3 → NP_114430.2  neurocalcin-delta

      See identical proteins and their annotated locations for NP_114430.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8) differs in the 5' UTR compared to variant 1.
      Source sequence(s)
      AL136612, AP000426, BC063428, BM681731, DA211806
      Consensus CDS
      CCDS6292.1
      UniProtKB/Swiss-Prot
      P29554, P61601, Q8IYC3, Q9H0W2
      UniProtKB/TrEMBL
      B2RB70, E5RGA9
      Related
      ENSP00000220931.6, ENST00000220931.11
      Conserved Domains (1) summary
      COG5126
      Location:14 → 179
      FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

      Range
      101686542..102124907 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047422315.1 → XP_047278271.1  neurocalcin-delta isoform X1

      UniProtKB/Swiss-Prot
      P29554, P61601, Q8IYC3, Q9H0W2
      UniProtKB/TrEMBL
      B2RB70, E5RGA9

    2. XM_047422305.1 → XP_047278261.1  neurocalcin-delta isoform X1

      UniProtKB/Swiss-Prot
      P29554, P61601, Q8IYC3, Q9H0W2
      UniProtKB/TrEMBL
      B2RB70, E5RGA9

    3. XM_047422304.1 → XP_047278260.1  neurocalcin-delta isoform X1

      UniProtKB/Swiss-Prot
      P29554, P61601, Q8IYC3, Q9H0W2
      UniProtKB/TrEMBL
      B2RB70, E5RGA9

    4. XM_047422317.1 → XP_047278273.1  neurocalcin-delta isoform X1

      UniProtKB/Swiss-Prot
      P29554, P61601, Q8IYC3, Q9H0W2
      UniProtKB/TrEMBL
      B2RB70, E5RGA9

    5. XM_047422316.1 → XP_047278272.1  neurocalcin-delta isoform X1

      UniProtKB/Swiss-Prot
      P29554, P61601, Q8IYC3, Q9H0W2
      UniProtKB/TrEMBL
      B2RB70, E5RGA9

    6. XM_047422303.1 → XP_047278259.1  neurocalcin-delta isoform X1

      UniProtKB/Swiss-Prot
      P29554, P61601, Q8IYC3, Q9H0W2
      UniProtKB/TrEMBL
      B2RB70, E5RGA9

    7. XM_047422318.1 → XP_047278274.1  neurocalcin-delta isoform X1

      UniProtKB/Swiss-Prot
      P29554, P61601, Q8IYC3, Q9H0W2
      UniProtKB/TrEMBL
      B2RB70, E5RGA9

    8. XM_047422311.1 → XP_047278267.1  neurocalcin-delta isoform X1

      UniProtKB/Swiss-Prot
      P29554, P61601, Q8IYC3, Q9H0W2
      UniProtKB/TrEMBL
      B2RB70, E5RGA9

    9. XM_047422306.1 → XP_047278262.1  neurocalcin-delta isoform X1

      UniProtKB/Swiss-Prot
      P29554, P61601, Q8IYC3, Q9H0W2
      UniProtKB/TrEMBL
      B2RB70, E5RGA9

    10. XM_047422307.1 → XP_047278263.1  neurocalcin-delta isoform X1

      UniProtKB/Swiss-Prot
      P29554, P61601, Q8IYC3, Q9H0W2
      UniProtKB/TrEMBL
      B2RB70, E5RGA9

    11. XM_047422314.1 → XP_047278270.1  neurocalcin-delta isoform X1

      UniProtKB/Swiss-Prot
      P29554, P61601, Q8IYC3, Q9H0W2
      UniProtKB/TrEMBL
      B2RB70, E5RGA9

    12. XM_047422313.1 → XP_047278269.1  neurocalcin-delta isoform X1

      UniProtKB/Swiss-Prot
      P29554, P61601, Q8IYC3, Q9H0W2
      UniProtKB/TrEMBL
      B2RB70, E5RGA9

    13. XM_047422308.1 → XP_047278264.1  neurocalcin-delta isoform X1

      UniProtKB/Swiss-Prot
      P29554, P61601, Q8IYC3, Q9H0W2
      UniProtKB/TrEMBL
      B2RB70, E5RGA9

    14. XM_047422312.1 → XP_047278268.1  neurocalcin-delta isoform X1

      UniProtKB/Swiss-Prot
      P29554, P61601, Q8IYC3, Q9H0W2
      UniProtKB/TrEMBL
      B2RB70, E5RGA9

    15. XM_047422319.1 → XP_047278275.1  neurocalcin-delta isoform X1

      UniProtKB/Swiss-Prot
      P29554, P61601, Q8IYC3, Q9H0W2
      UniProtKB/TrEMBL
      B2RB70, E5RGA9

    16. XM_047422309.1 → XP_047278265.1  neurocalcin-delta isoform X1

      UniProtKB/Swiss-Prot
      P29554, P61601, Q8IYC3, Q9H0W2
      UniProtKB/TrEMBL
      B2RB70, E5RGA9

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060932.1 Alternate T2T-CHM13v2.0

      Range
      102812429..103250775 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P61601.2 GenPept UniProtKB/Swiss-Prot:P61601

    Gene LinkOut

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