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    NALCN sodium leak channel, non-selective [ Homo sapiens (human) ]

    Gene ID: 259232, updated on 27-Apr-2017
    Official Symbol
    NALCNprovided by HGNC
    Official Full Name
    sodium leak channel, non-selectiveprovided by HGNC
    Primary source
    HGNC:HGNC:19082
    See related
    Ensembl:ENSG00000102452 MIM:611549; Vega:OTTHUMG00000017295
    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
    Also known as
    IHPRF; INNFD; CanIon; IHPRF1; VGCNL1; CLIFAHDD; bA430M15.1
    Summary
    This gene encodes a voltage-independent, nonselective cation channel which belongs to a family of voltage-gated sodium and calcium channels that regulates the resting membrane potential and excitability of neurons. This family is expressed throughout the nervous system and conducts a persistent sodium leak current that contributes to tonic neuronal excitability. The encoded protein forms a channelosome complex that includes G-protein-coupled receptors, UNC-79, UNC-80, NCA localization factor-1, and src family tyrosine kinases. Naturally occurring mutations in this gene are associated with infantile neuroaxonal dystrophy, infantile hypotonia with psychomotor retardation and characteristic facies (IHPRF) syndrome, and congenital contractures of the limbs and face with hypotonia and developmental delay (CLIFAHDD) syndrome. A knockout of the orthologous gene in mice results in paralysis with a severely disrupted respiratory rhythm, and lethality within 24 hours after birth. [provided by RefSeq, Apr 2017]
    Orthologs
    Location:
    13q32.3-q33.1
    Exon count:
    47
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 13 NC_000013.11 (101053774..101417206, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (101706130..102068813, complement)

    Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene NALCN antisense RNA 1 Neighboring gene ADP ribosylation factor 4 pseudogene 3 Neighboring gene long intergenic non-protein coding RNA 411 Neighboring gene integrin subunit beta like 1 Neighboring gene uncharacterized LOC107984616 Neighboring gene RNA, U1 small nuclear 24, pseudogene Neighboring gene fibroblast growth factor 14

    • 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 Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    NHGRI GWAS Catalog

    Description
    A genome-wide meta-analysis identifies novel loci associated with schizophrenia and bipolar disorder.
    NHGRI GWA Catalog
    Genome-wide association study of atypical psychosis.
    NHGRI GWA Catalog
    Genome-wide association study of neurocognitive impairment and dementia in HIV-infected adults.
    NHGRI GWA Catalog
    Prognostic implications of genetic variants in advanced non-small cell lung cancer: a genome-wide association study.
    NHGRI GWA Catalog
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • FLJ23913, FLJ44659, FLJ44764, MGC74524

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    cation channel activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    cation channel activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    leak channel activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    sodium channel activity TAS
    Traceable Author Statement
    more info
     
    voltage-gated ion channel activity IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    calcium ion transmembrane transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    calcium ion transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    ion transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    ion transmembrane transport TAS
    Traceable Author Statement
    more info
     
    membrane depolarization during action potential IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    potassium ion transmembrane transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    regulation of ion transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of resting membrane potential ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    sodium ion transmembrane transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    integral component of membrane IEA
    Inferred from Electronic Annotation
    more info
     
    plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    plasma membrane TAS
    Traceable Author Statement
    more info
     
    Preferred Names
    sodium leak channel non-selective protein
    Names
    four repeat voltage-gated ion channel
    voltage gated channel like 1

    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.

    Genomic

    1. NG_053176.1 RefSeqGene

      Range
      5699..368433
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001350748.1NP_001337677.1  sodium leak channel non-selective protein isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AL138707, AL354891, AL356778, BF516239, KF511189
    2. NM_001350749.1NP_001337678.1  sodium leak channel non-selective protein isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site in the 5' UTR and lacks an alternate exon in the 5' coding region but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1. Both variants 2 and 3 encode the same isoform (2).
      Source sequence(s)
      AL138707, AL354891, AL356778, BF516239, KF511189
    3. NM_001350750.1NP_001337679.1  sodium leak channel non-selective protein isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks two alternate exons in the 5' coding region but maintains the reading frame, compared to variant 1. The encoded isoform (3) is shorter than isoform 1. Both variants 4 and 5 encode the same isoform (3).
      Source sequence(s)
      AL138707, AL354891, AL356778, BF516239, KF511189
    4. NM_001350751.1NP_001337680.1  sodium leak channel non-selective protein isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) uses an alternate splice site in the 5' UTR and lacks two alternate exons in the 5' coding region but maintains the reading frame, compared to variant 1. The encoded isoform (3) is shorter than isoform 1. Both variants 4 and 5 encode the same isoform (3).
      Source sequence(s)
      AL138707, AL354891, AL356778, BF516239, KF511189
    5. NM_052867.3NP_443099.1  sodium leak channel non-selective protein isoform 2

      See identical proteins and their annotated locations for NP_443099.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate exon in the 5' coding region but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1. Both variants 2 and 3 encode the same isoform (2).
      Source sequence(s)
      AK002089, AL356778, AY141972, BC012128, BF516239, DA128114
      Consensus CDS
      CCDS9498.1
      UniProtKB/Swiss-Prot
      Q8IZF0
      UniProtKB/TrEMBL
      A0A024RE05, B3KMK1
      Related
      ENSP00000251127.6, OTTHUMP00000018654, ENST00000251127.10
      Conserved Domains (2) summary
      pfam00520
      Location:12341458
      Ion_trans; Ion transport protein
      pfam10688
      Location:12661411
      Imp-YgjV; Bacterial inner membrane protein

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000013.11 Reference GRCh38.p7 Primary Assembly

      Range
      101053774..101417206 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011521067.2XP_011519369.1  sodium leak channel non-selective protein isoform X1

      Conserved Domains (2) summary
      pfam00520
      Location:12531477
      Ion_trans; Ion transport protein
      pfam10688
      Location:12851430
      Imp-YgjV; Bacterial inner membrane protein
    2. XM_011521069.2XP_011519371.1  sodium leak channel non-selective protein isoform X3

      Conserved Domains (2) summary
      pfam00520
      Location:12241448
      Ion_trans; Ion transport protein
      pfam10688
      Location:12561401
      Imp-YgjV; Bacterial inner membrane protein
    3. XM_011521068.2XP_011519370.1  sodium leak channel non-selective protein isoform X2

      See identical proteins and their annotated locations for XP_011519370.1

      UniProtKB/Swiss-Prot
      Q8IZF0
      UniProtKB/TrEMBL
      A0A024RE05
      Conserved Domains (2) summary
      pfam00520
      Location:12341458
      Ion_trans; Ion transport protein
      pfam10688
      Location:12661411
      Imp-YgjV; Bacterial inner membrane protein
    4. XM_017020535.1XP_016876024.1  sodium leak channel non-selective protein isoform X4

    5. XM_017020534.1XP_016876023.1  sodium leak channel non-selective protein isoform X4

    6. XM_017020536.1XP_016876025.1  sodium leak channel non-selective protein isoform X5

    7. XM_017020537.1XP_016876026.1  sodium leak channel non-selective protein isoform X6

    Alternate CHM1_1.1

    Genomic

    1. NC_018924.2 Alternate CHM1_1.1

      Range
      101676115..102038862 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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