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

    Gene ID: 259232, updated on 17-Jun-2024

    Summary

    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; AllianceGenome:HGNC:19082
    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]
    Expression
    Biased expression in brain (RPKM 11.1), adrenal (RPKM 2.5) and 5 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See NALCN in Genome Data Viewer
    Location:
    13q32.3-q33.1
    Exon count:
    48
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (101053776..101417179, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (100268892..100632422, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (101706128..102068859, complement)

    Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene NALCN antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 9290 Neighboring gene ADP ribosylation factor 4 pseudogene 3 Neighboring gene long intergenic non-protein coding RNA 411 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:101698875-101699376 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr13:101701141-101702340 Neighboring gene uncharacterized LOC124903202 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:101717146-101717646 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:101717647-101718147 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr13:101909917-101911116 Neighboring gene NANOG hESC enhancer GRCh37_chr13:101986545-101987100 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:102068211-102068761 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:102067660-102068210 Neighboring gene Sharpr-MPRA regulatory region 15039 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr13:102102071-102103270 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:102104604-102105108 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:102126208-102126708 Neighboring gene Sharpr-MPRA regulatory region 3234 Neighboring gene integrin subunit beta like 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr13:102341159-102341390 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr13:102360299-102360823 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7963 Neighboring gene NANOG hESC enhancer GRCh37_chr13:102403785-102404286 Neighboring gene fibroblast growth factor 14 Neighboring gene RNA, U1 small nuclear 24, pseudogene

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    A genome-wide meta-analysis identifies novel loci associated with schizophrenia and bipolar disorder.
    EBI GWAS Catalog
    Genome-wide association study of atypical psychosis.
    EBI GWAS Catalog
    Genome-wide association study of neurocognitive impairment and dementia in HIV-infected adults.
    EBI GWAS Catalog
    Prognostic implications of genetic variants in advanced non-small cell lung cancer: a genome-wide association study.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ23913, FLJ44659, FLJ44764, MGC74524

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables leak channel activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables monoatomic cation channel activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables monoatomic cation channel activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables sodium channel activity TAS
    Traceable Author Statement
    more info
     
    enables voltage-gated sodium channel activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables voltage-gated sodium channel activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in calcium ion transmembrane transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in monoatomic ion transmembrane transport TAS
    Traceable Author Statement
    more info
     
    involved_in positive regulation of synaptic transmission, GABAergic IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of synaptic transmission, cholinergic IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in potassium ion transmembrane transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of resting membrane potential ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in sodium ion transmembrane transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    part_of monoatomic ion channel complex IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    sodium leak channel NALCN
    Names
    four repeat voltage-gated ion channel
    voltage gated channel like 1

    NCBI Reference Sequences (RefSeq)

    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.

    Genomic

    1. NG_053176.1 RefSeqGene

      Range
      5699..368431
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001350748.2NP_001337677.1  sodium leak channel NALCN 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
      Consensus CDS
      CCDS91832.1
      UniProtKB/TrEMBL
      A0A6Q8PFS9, A0A976XH31
      Related
      ENSP00000501955.1, ENST00000675332.1
      Conserved Domains (1) summary
      pfam00520
      Location:9161190
      Ion_trans; Ion transport protein
    2. NM_001350749.2NP_001337678.1  sodium leak channel NALCN 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
      Consensus CDS
      CCDS9498.1
      UniProtKB/Swiss-Prot
      Q6P2S6, Q6ZMI7, Q8IZF0, Q8IZZ1, Q8TAH1
      UniProtKB/TrEMBL
      A0A976XH31
      Conserved Domains (1) summary
      pfam00520
      Location:8871161
      Ion_trans; Ion transport protein
    3. NM_001350750.2NP_001337679.1  sodium leak channel NALCN 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
      Consensus CDS
      CCDS91831.1
      UniProtKB/TrEMBL
      A0A6Q8PF19, A0A976XH31
      Related
      ENSP00000501603.1, ENST00000676315.1
      Conserved Domains (1) summary
      pfam00520
      Location:8581132
      Ion_trans; Ion transport protein
    4. NM_001350751.2NP_001337680.1  sodium leak channel NALCN 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
      Consensus CDS
      CCDS91831.1
      UniProtKB/TrEMBL
      A0A6Q8PF19, A0A976XH31
      Conserved Domains (1) summary
      pfam00520
      Location:8581132
      Ion_trans; Ion transport protein
    5. NM_052867.4NP_443099.1  sodium leak channel NALCN 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
      Q6P2S6, Q6ZMI7, Q8IZF0, Q8IZZ1, Q8TAH1
      UniProtKB/TrEMBL
      A0A976XH31
      Related
      ENSP00000251127.6, ENST00000251127.11
      Conserved Domains (1) summary
      pfam00520
      Location:8871161
      Ion_trans; Ion transport protein

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000013.11 Reference GRCh38.p14 Primary Assembly

      Range
      101053776..101417179 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011521069.3XP_011519371.1  sodium leak channel NALCN isoform X2

      UniProtKB/TrEMBL
      A0A976XH31
      Conserved Domains (2) summary
      pfam00520
      Location:12241448
      Ion_trans; Ion transport protein
      pfam10688
      Location:12561401
      Imp-YgjV; Bacterial inner membrane protein
    2. XM_011521067.3XP_011519369.1  sodium leak channel NALCN isoform X1

      UniProtKB/TrEMBL
      A0A976XH31
      Conserved Domains (2) summary
      pfam00520
      Location:12531477
      Ion_trans; Ion transport protein
      pfam10688
      Location:12851430
      Imp-YgjV; Bacterial inner membrane protein
    3. XM_024449336.2XP_024305104.1  sodium leak channel NALCN isoform X5

      UniProtKB/TrEMBL
      A0A976XH31
      Conserved Domains (1) summary
      pfam00520
      Location:9351209
      Ion_trans; Ion transport protein
    4. XM_017020536.3XP_016876025.1  sodium leak channel NALCN isoform X3

      UniProtKB/TrEMBL
      A0A976XH31
    5. XM_017020537.2XP_016876026.1  sodium leak channel NALCN isoform X4

      UniProtKB/TrEMBL
      A0A976XH31

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060937.1 Alternate T2T-CHM13v2.0

      Range
      100268892..100632422 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054374412.1XP_054230387.1  sodium leak channel NALCN isoform X1

      UniProtKB/TrEMBL
      A0A976XH31
    2. XM_054374416.1XP_054230391.1  sodium leak channel NALCN isoform X5

      UniProtKB/TrEMBL
      A0A976XH31
    3. XM_054374413.1XP_054230388.1  sodium leak channel NALCN isoform X2

      UniProtKB/TrEMBL
      A0A976XH31
    4. XM_054374414.1XP_054230389.1  sodium leak channel NALCN isoform X3

      UniProtKB/TrEMBL
      A0A976XH31
    5. XM_054374415.1XP_054230390.1  sodium leak channel NALCN isoform X4

      UniProtKB/TrEMBL
      A0A976XH31