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    POLR1C RNA polymerase I and III subunit C [ Homo sapiens (human) ]

    Gene ID: 9533, updated on 3-Nov-2024

    Summary

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    Official Symbol
    POLR1Cprovided by HGNC
    Official Full Name
    RNA polymerase I and III subunit Cprovided by HGNC
    Primary source
    HGNC:HGNC:20194
    See related
    Ensembl:ENSG00000171453 MIM:610060; AllianceGenome:HGNC:20194
    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
    AC40; RPA5; TCS3; HLD11; RPA39; RPA40; RPAC1; RPC40
    Summary
    The protein encoded by this gene is a subunit of both RNA polymerase I and RNA polymerase III complexes. The encoded protein is part of the Pol core element. Mutations in this gene have been associated with Treacher Collins syndrome (TCS) and hypomyelinating leukodystrophy 11. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]
    Expression
    Ubiquitous expression in testis (RPKM 7.7), skin (RPKM 5.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See POLR1C in Genome Data Viewer
    Location:
    6p21.1
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (43517089..43562407)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (43345828..43391139)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (43484827..43530144)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17233 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17234 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24602 Neighboring gene leucine rich repeat containing 73 Neighboring gene Yip1 domain family member 3 Neighboring gene MPRA-validated peak5815 silencer Neighboring gene exportin 5 Neighboring gene U7 small nuclear RNA Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17235 Neighboring gene small Cajal body-specific RNA 15 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:43514706-43515905 Neighboring gene ribosomal protein S2 pseudogene 29 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24603 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17236 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24604 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43545520-43546020 Neighboring gene DNA polymerase eta Neighboring gene ReSE screen-validated silencer GRCh37_chr6:43579698-43579923 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17237 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17238 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24605 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24606 Neighboring gene GTP binding protein 2 Neighboring gene MAD2L1 binding protein Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43604555-43605342 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43605343-43606129

    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 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. Recessive mutations in POLR1C cause a leukodystrophy by impairing biogenesis of RNA polymerase III. Thiffault I, et al. Nat Commun, 2015 Jul 7. PMID 26151409, Free PMC Article
    2. Treacher Collins syndrome 3 (TCS3)-associated POLR1C mutants are localized in the lysosome and inhibits chondrogenic differentiation. Matsumoto N, et al. Biochem Biophys Res Commun, 2018 Apr 30. PMID 29567474
    3. Autosomal recessive Treacher Collins syndrome due to POLR1C mutations: Report of a new family and review of the literature. Ghesh L, et al. Am J Med Genet A, 2019 Jul. PMID 30957429
    4. Novel POLR1C mutation in RNA polymerase III-related leukodystrophy with severe myoclonus and dystonia. Kraoua I, et al. Mol Genet Genomic Med, 2019 Sep. PMID 31368241, Free PMC Article
    5. Cloning and characterization of the human RNA polymerase I subunit hRPA40. Dammann R, et al. Biochim Biophys Acta, 1998 Mar 9. PMID 9540830

    See all (148) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Endocrine and Growth Abnormalities in 4H Leukodystrophy Caused by Variants in POLR3A, POLR3B, and POLR1C.
      Title: Endocrine and Growth Abnormalities in 4H Leukodystrophy Caused by Variants in POLR3A, POLR3B, and POLR1C.
    2. Combined Genome, Transcriptome and Metabolome Analysis in the Diagnosis of Childhood Cerebellar Ataxia.
      Title: Combined Genome, Transcriptome and Metabolome Analysis in the Diagnosis of Childhood Cerebellar Ataxia.
    3. eport here a new family with two sisters affected by mild TCS carrying compound POLR1C heterozygous mutations, and review the literature on mild forms of TCS, autosomal recessive inheritance in this syndrome and POLR1C mutations
      Title: Autosomal recessive Treacher Collins syndrome due to POLR1C mutations: Report of a new family and review of the literature.
    4. The clinical and imaging findings of patients with POLR1C hypomyelinating leukodystrophy are reviewed. Interestingly, severe myoclonic dystonia and T2 hypointensity of the substantia nigra and the subthalamic nucleus are not reported yet and could be helpful for the diagnosis of POLR1C hypomyelinating leukodystrophy.
      Title: Novel POLR1C mutation in RNA polymerase III-related leukodystrophy with severe myoclonus and dystonia.
    5. Treacher Collins syndrome 3-associated mutation leads to the localization of POLR1C into the lysosome and inhibits chondrogenic differentiation, possibly explaining a portion of the pathological molecular basis underlying Treacher Collins syndrome.
      Title: Treacher Collins syndrome 3 (TCS3)-associated POLR1C mutants are localized in the lysosome and inhibits chondrogenic differentiation.
    6. We report a clinical and extensive molecular study, including TCOF1, POLR1D, POLR1C, and EFTUD2 genes, in a series of 146 patients with TCS.
      Title: Treacher Collins syndrome: a clinical and molecular study based on a large series of patients.
    7. This study is the first to show that distinct mutations in a gene coding for a shared subunit of two RNA polymerases lead to selective modification of the enzymes' availability leading to two different clinical conditions.
      Title: Recessive mutations in POLR1C cause a leukodystrophy by impairing biogenesis of RNA polymerase III.
    8. Mutations in TCOF1, POLR1C and POLR1D have all been implicated in causing TCS
      Title: Treacher Collins Syndrome: the genetics of a craniofacial disease.
    9. mutations in both alleles of POLR1C in three individuals with Treacher Collins syndrome.
      Title: Mutations in genes encoding subunits of RNA polymerases I and III cause Treacher Collins syndrome.
    10. analyzed the kinetics of assembly and elongation of the RNA polymerase I complex on endogenous ribosomal genes in the nuclei of living cells with the use of in vivo microscopy
      Title: A kinetic framework for a mammalian RNA polymerase in vivo.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Hypomyelinating leukodystrophy 11
    MedGen: C4225305 OMIM: 616494 GeneReviews: POLR3-Related Leukodystrophy
    		not available
    Treacher Collins syndrome 3
    MedGen: C1855433 OMIM: 248390 GeneReviews: Treacher Collins Syndrome
    		not available

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA-directed 5'-3' RNA polymerase activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    contributes_to RNA polymerase I activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    contributes_to RNA polymerase III activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein dimerization activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in transcription by RNA polymerase I TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in transcription by RNA polymerase III IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of RNA polymerase I complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of RNA polymerase I complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of RNA polymerase III complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of RNA polymerase III complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in fibrillar center IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    DNA-directed RNA polymerases I and III subunit RPAC1
    Names
    DNA-directed RNA polymerase I subunit C
    DNA-directed RNA polymerases I and III 40 kDa polypeptide
    RNA polymerase I subunit C
    RNA polymerases I and III subunit AC1
    polymerase (RNA) I polypeptide C, 30kDa
    polymerase (RNA) I subunit C

    NCBI Reference Sequences (RefSeq)

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    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_028283.4 RefSeqGene

      Range
      5002..9426
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001318876.2 → NP_001305805.1  DNA-directed RNA polymerases I and III subunit RPAC1 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 3' terminal exon, resulting in a different 3' coding region and 3' UTR compared to variant 1. The encoded isoform (2) has a shorter, distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AF047441, BC008863, DW415914
      UniProtKB/TrEMBL
      A0A2R8Y5D3
      Related
      ENSP00000307212.3, ENST00000304004.7
      Conserved Domains (2) summary
      cd07032
      Location:49 → 307
      RNAP_I_II_AC40; AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III
      smart00662
      Location:61 → 267
      RPOLD; RNA polymerases D

    2. NM_001363658.2 → NP_001350587.1  DNA-directed RNA polymerases I and III subunit RPAC1 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (3) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AL355802
      Consensus CDS
      CCDS87408.1
      UniProtKB/TrEMBL
      A0A2R8Y5D3, A0A2R8YEZ4
      Related
      ENSP00000496018.1, ENST00000643341.1
      Conserved Domains (1) summary
      cd07032
      Location:49 → 307
      RNAP_I_II_AC40; AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III

    3. NM_203290.4 → NP_976035.1  DNA-directed RNA polymerases I and III subunit RPAC1 isoform 1

      See identical proteins and their annotated locations for NP_976035.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      BC008863, DW415914
      Consensus CDS
      CCDS4901.1
      UniProtKB/Swiss-Prot
      O15160, O75395, Q5JTE3
      UniProtKB/TrEMBL
      Q96HT3
      Related
      ENSP00000496044.1, ENST00000642195.1
      Conserved Domains (1) summary
      cd07032
      Location:49 → 339
      RNAP_I_II_AC40; AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      43517089..43562407
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      43345828..43391139
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_004875.2: Suppressed sequence

      Description
      NM_004875.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O15160.1 GenPept UniProtKB/Swiss-Prot:O15160

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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