POLR1E

RNA polymerase I subunit E, the group of RNA polymerase subunits

Basic information

Region (hg38): 9:37485948-37503697

Previous symbols: [ "PRAF1" ]

Links

ENSG00000137054 ∙ NCBI:64425 ∙ ∙ HGNC:17631 ∙ Uniprot:Q9GZS1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the POLR1E gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the POLR1E gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	0	0

Variants in POLR1E

This is a list of pathogenic ClinVar variants found in the POLR1E region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
9-37486055-C-T		not specified	Uncertain significance (May 21, 2024)
9-37486099-G-A		not specified	Uncertain significance (Feb 16, 2023)
9-37486744-C-A		not specified	Uncertain significance (Apr 09, 2024)
9-37486756-T-C		not specified	Uncertain significance (Feb 06, 2023)
9-37486783-A-G		not specified	Uncertain significance (Mar 01, 2023)
9-37487900-A-G		not specified	Uncertain significance (Apr 28, 2023)
9-37489353-T-C		not specified	Uncertain significance (Dec 14, 2021)
9-37492659-G-A		not specified	Uncertain significance (Oct 12, 2022)
9-37492668-G-A		not specified	Uncertain significance (Dec 03, 2024)
9-37492681-C-T		not specified	Uncertain significance (Oct 12, 2021)
9-37493673-G-A		not specified	Uncertain significance (Apr 19, 2023)
9-37493679-A-G		not specified	Uncertain significance (Mar 18, 2024)
9-37493689-C-T		not specified	Uncertain significance (Dec 01, 2022)
9-37495258-G-A		not specified	Uncertain significance (Mar 25, 2024)
9-37495271-A-G		not specified	Uncertain significance (Aug 05, 2024)
9-37495920-A-G		not specified	Uncertain significance (May 23, 2023)
9-37495941-G-A		not specified	Uncertain significance (Nov 28, 2023)
9-37495946-G-A		not specified	Uncertain significance (Jul 25, 2023)
9-37495974-T-C		not specified	Uncertain significance (Jun 28, 2023)
9-37495984-C-A		not specified	Uncertain significance (Jun 06, 2023)
9-37498200-G-A		not specified	Uncertain significance (Jul 14, 2021)
9-37500845-C-G		not specified	Uncertain significance (May 20, 2024)
9-37501732-G-T		not specified	Uncertain significance (Dec 13, 2022)
9-37503046-G-T		not specified	Uncertain significance (May 14, 2024)
9-37503085-A-C		not specified	Uncertain significance (Oct 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
POLR1E	protein_coding	protein_coding	ENST00000377798	12	17763

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.74e-7	0.946	125687	0	61	125748	0.000243

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.741	204	236	0.864	0.0000127	2747
Missense in Polyphen		33	50.305	0.656		593
Synonymous	1.55	72	90.8	0.793	0.00000513	788
Loss of Function	1.87	14	23.9	0.587	0.00000142	270

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000569	0.000569
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000319	0.000316
Middle Eastern	0.000110	0.000109
South Asian	0.000132	0.000131
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors. Appears to be involved in the formation of the initiation complex at the promoter by mediating the interaction between Pol I and UBTF/UBF (By similarity). {ECO:0000250}.
• Pathway: Pyrimidine metabolism - Homo sapiens (human);RNA polymerase - Homo sapiens (human);Purine metabolism - Homo sapiens (human);Pyrimidine metabolism;Eukaryotic Transcription Initiation;B-WICH complex positively regulates rRNA expression;Positive epigenetic regulation of rRNA expression;NoRC negatively regulates rRNA expression;Negative epigenetic regulation of rRNA expression;Epigenetic regulation of gene expression;Gene expression (Transcription);RNA Polymerase I Promoter Clearance;Purine metabolism;RNA Polymerase I Transcription Termination;RNA Polymerase I Transcription;RNA Polymerase I Transcription Initiation;RNA Polymerase I Promoter Escape;Pyrimidine metabolism;RNA Polymerase I Chain Elongation;TNFalpha (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.862
• rvis_EVS: 0.42
• rvis_percentile_EVS: 77.16

Haploinsufficiency Scores

• pHI: 0.655
• hipred: Y
• hipred_score: 0.658
• ghis: 0.473

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.980

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Polr1e
• Phenotype: growth/size/body region phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype

Gene ontology

• Biological process: RNA polymerase I preinitiation complex assembly;transcription initiation from RNA polymerase I promoter;termination of RNA polymerase I transcription;positive regulation of gene expression, epigenetic
• Cellular component: fibrillar center;nucleus;nucleoplasm;nucleolus;RNA polymerase I complex
• Molecular function: RNA polymerase I activity;RNA polymerase I general transcription initiation factor binding;DNA binding