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POLR1D RNA polymerase I and III subunit D [ Homo sapiens (human) ]

Gene ID: 51082, updated on 13-Apr-2024

Summary

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Official Symbol
POLR1Dprovided by HGNC
Official Full Name
RNA polymerase I and III subunit Dprovided by HGNC
Primary source
HGNC:HGNC:20422
See related
Ensembl:ENSG00000186184 MIM:613715; AllianceGenome:HGNC:20422
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
AC19; RPA9; TCS2; RPA16; RPAC2; RPC16; POLR1C; RPO1-3
Summary
The protein encoded by this gene is a component of the RNA polymerase I and RNA polymerase III complexes, which function in the synthesis of ribosomal RNA precursors and small RNAs, respectively. Mutations in this gene are a cause of Treacher Collins syndrome (TCS), a craniofacial development disorder. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2011]
Expression
Ubiquitous expression in testis (RPKM 19.3), adrenal (RPKM 13.6) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
13q12.2
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (27620743..27667411)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (26841857..26888521)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (28194880..28241548)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr13:28008622-28009821 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_32805 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:28023938-28024852 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7506 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7507 Neighboring gene general transcription factor IIIA Neighboring gene Sharpr-MPRA regulatory region 13742 Neighboring gene mitochondrial translational initiation factor 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7508 Neighboring gene RNA, U6 small nuclear 63, pseudogene Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_32806 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_32807 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_32809 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:28107144-28107644 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:28107645-28108145 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_32810 Neighboring gene ligand of numb-protein X 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:28194694-28195422 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5204 Neighboring gene nucleophosmin 1 pseudogene 4 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr13:28302713-28303912 Neighboring gene uncharacterized LOC105370129

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. Cell-free DNA analysis reveals POLR1D-mediated resistance to bevacizumab in colorectal cancer. Zhou Q, et al. Genome Med, 2020 Feb 22. PMID 32087735, Free PMC Article
  2. Expression and Clinical Significance of POLR1D in Colorectal Cancer. Tian Y, et al. Oncology, 2020. PMID 31722331
  3. POLR1D promotes colorectal cancer progression and predicts poor prognosis of patients. Wang M, et al. Mol Carcinog, 2019 May. PMID 30582221
  4. Whole exome sequencing identifies a POLRID mutation segregating in a father and two daughters with findings of Klippel-Feil and Treacher Collins syndromes. Giampietro PF, et al. Am J Med Genet A, 2015 Jan. PMID 25348728
  5. Association of survival and disease progression with chromosomal instability: a genomic exploration of colorectal cancer. Sheffer M, et al. Proc Natl Acad Sci U S A, 2009 Apr 28. PMID 19359472, Free PMC Article

See all (65) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. A clinically-relevant residue of POLR1D is required for Drosophila development.
    Title: A clinically-relevant residue of POLR1D is required for Drosophila development.
  2. POLR1B and neural crest cell anomalies in Treacher Collins syndrome type 4.
    Title: POLR1B and neural crest cell anomalies in Treacher Collins syndrome type 4.
  3. Cell-free DNA analysis reveals POLR1D-mediated resistance to bevacizumab in colorectal cancer.
    Title: Cell-free DNA analysis reveals POLR1D-mediated resistance to bevacizumab in colorectal cancer.
  4. High POLR1D expression is an independent prognostic factor for poor overall survival in colorectal cancer.
    Title: Expression and Clinical Significance of POLR1D in Colorectal Cancer.
  5. High POLR1D expression is associated with colorectal cancer progression.
    Title: POLR1D promotes colorectal cancer progression and predicts poor prognosis of patients.
  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. Whole exome sequencing identified a nonsynonymous mutation in POLR1D (subunit of RNA polymerase I and II): exon2:c.T332C:p.L111P.
    Title: Whole exome sequencing identifies a POLRID mutation segregating in a father and two daughters with findings of Klippel-Feil and Treacher Collins syndromes.
  8. Autosomal recessive POLR1D mutation with decrease of TCOF1 mRNA is responsible for Treacher Collins syndrome.
    Title: Autosomal recessive POLR1D mutation with decrease of TCOF1 mRNA is responsible for Treacher Collins syndrome.
  9. Mutations in TCOF1, POLR1C and POLR1D have all been implicated in causing TCS
    Title: Treacher Collins Syndrome: the genetics of a craniofacial disease.
  10. Characterization of the homologous mouse protein.
    Title: Mouse RNA polymerase I 16-kDa subunit able to associate with 40-kDa subunit is a homolog of yeast AC19 subunit of RNA polymerases I and III.
Submit: New GeneRIF Correction See all GeneRIFs (13)

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

Associated conditions

Description Tests
Treacher Collins syndrome 2
MedGen: C3150983 OMIM: 613717 GeneReviews: Treacher Collins Syndrome
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Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2021-06-23)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2021-06-23)

ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
Common variants on 14q32 and 13q12 are associated with DLBCL susceptibility.
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)

Genotypes

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

Clone Names

  • MGC9850, FLJ20616

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
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 III IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in transcription elongation by RNA polymerase I IBA
Inferred from Biological aspect of Ancestor
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 

General protein information

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Preferred Names
DNA-directed RNA polymerases I and III subunit RPAC2; Protein POLR1D
Names
DNA-directed RNA polymerase I subunit D
RNA polymerase I subunit D
RNA polymerases I and III subunit AC2
polymerase (RNA) I polypeptide D, 16kDa
polymerase (RNA) I subunit D

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_028908.1 RefSeqGene

    Range
    6150..7707
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001206559.2 → NP_001193488.1  DNA-directed RNA polymerases I and III subunit RPAC2 isoform 3

    See identical proteins and their annotated locations for NP_001193488.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in both UTRs and in the coding region, compared to variant 1. The encoded isoform (3) shares identity with isoform 2 but is distinct and shorter, compared to isoform 1.
    Source sequence(s)
    AK307356, BC015319, BQ004736, DB123903, DR156229
    Consensus CDS
    CCDS73555.1
    UniProtKB/TrEMBL
    A0A087WTY1, A0A8I5QL02
    Related
    ENSP00000478213.1, ENST00000621089.2

  2. NM_001374407.1 → NP_001361336.1  DNA-directed RNA polymerases I and III subunit RPAC2 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AL136439
    Consensus CDS
    CCDS9325.1
    UniProtKB/Swiss-Prot
    P0DPB6, Q5TBX2, Q96BR3, Q9Y2S0
    UniProtKB/TrEMBL
    A0A0R4J2F3
    Conserved Domains (1) summary
    cd07029
    Location:30 → 114
    RNAP_I_III_AC19; AC19 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III

  3. NM_015972.4 → NP_057056.1  DNA-directed RNA polymerases I and III subunit RPAC2 isoform 1

    See identical proteins and their annotated locations for NP_057056.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the shortest transcript but encodes the longest isoform (1).
    Source sequence(s)
    BC000889
    Consensus CDS
    CCDS9325.1
    UniProtKB/Swiss-Prot
    P0DPB6, Q5TBX2, Q96BR3, Q9Y2S0
    UniProtKB/TrEMBL
    A0A0R4J2F3
    Related
    ENSP00000302478.4, ENST00000302979.5
    Conserved Domains (1) summary
    cd07029
    Location:30 → 114
    RNAP_I_III_AC19; AC19 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III

  4. NM_152705.3 → NP_689918.1  Protein POLR1D isoform 2

    See identical proteins and their annotated locations for NP_689918.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (2) has a distinct and shorter C-terminus, compared to isoform 1.
    Source sequence(s)
    BC015319, BQ004736
    Consensus CDS
    CCDS9324.1
    UniProtKB/Swiss-Prot
    P0DPB5
    Related
    ENSP00000382604.3, ENST00000399697.7

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
    27620743..27667411
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047430381.1 → XP_047286337.1  Protein POLR1D isoform X2

    UniProtKB/Swiss-Prot
    P0DPB5

  2. XM_017020622.2 → XP_016876111.1  Protein POLR1D isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    26841857..26888521
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054374597.1 → XP_054230572.1  Protein POLR1D isoform X2

    UniProtKB/Swiss-Prot
    P0DPB5

  2. XM_054374596.1 → XP_054230571.1  Protein POLR1D isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P0DPB5.1 GenPept UniProtKB/Swiss-Prot:P0DPB5
P0DPB6.1 GenPept UniProtKB/Swiss-Prot:P0DPB6

Gene LinkOut

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

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