POLR2C

RNA polymerase II subunit C, the group of RNA polymerase subunits

Basic information

Region (hg38): 16:57462660-57472009

Links

ENSG00000102978 ∙ NCBI:5432 ∙ OMIM:180663 ∙ HGNC:9189 ∙ Uniprot:P19387 ∙ 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 POLR2C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the POLR2C 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			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	0

Variants in POLR2C

This is a list of pathogenic ClinVar variants found in the POLR2C region.

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

Position	Type	Phenotype	Significance	ClinVar
16-57462752-C-T		not specified	Uncertain significance (Jun 28, 2024)
16-57462759-C-T		not specified	Uncertain significance (Jun 17, 2024)
16-57462801-C-G		Genetic non-acquired premature ovarian failure	Likely pathogenic (Oct 01, 2019)
16-57463029-G-T		not specified	Likely benign (May 16, 2024)
16-57463037-A-G		not specified	Uncertain significance (Apr 19, 2023)
16-57463046-G-T		not specified	Uncertain significance (Apr 17, 2023)
16-57463060-G-C		not specified	Uncertain significance (Mar 19, 2024)
16-57463069-C-G		not specified	Uncertain significance (Oct 21, 2024)
16-57469719-C-T		not specified	Uncertain significance (Nov 08, 2024)
16-57469731-A-G		not specified	Uncertain significance (Sep 26, 2023)
16-57470006-G-C		not specified	Uncertain significance (Jun 22, 2024)
16-57470012-A-G		not specified	Uncertain significance (Dec 19, 2022)
16-57470065-G-T		Genetic non-acquired premature ovarian failure	Likely pathogenic (Oct 01, 2019)
16-57470066-T-C		Deafness;Infertility disorder	Uncertain significance (Apr 11, 2018)
16-57470069-C-T		not specified	Uncertain significance (Jan 31, 2022)
16-57470330-A-G		not specified	Uncertain significance (Dec 22, 2023)
16-57470341-G-A		not specified	Uncertain significance (Jul 13, 2022)
16-57470986-A-G		not specified	Uncertain significance (Nov 14, 2024)
16-57471010-G-A		not specified	Uncertain significance (Aug 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
POLR2C	protein_coding	protein_coding	ENST00000219252	9	9624

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00146	0.992	125737	0	11	125748	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.86	97	164	0.591	0.00000920	1798
Missense in Polyphen		30	56.963	0.52666		687
Synonymous	1.14	55	66.8	0.823	0.00000397	512
Loss of Function	2.40	8	19.4	0.413	0.00000114	194

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000220	0.000213
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000460	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.0000328	0.0000327
Other	0.00	0.00

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 II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB3 is part of the core element with the central large cleft and the clamp element that moves to open and close the cleft (By similarity). {ECO:0000250, ECO:0000269|PubMed:9852112}.
• Pathway: Pyrimidine metabolism - Homo sapiens (human);Huntington,s disease - Homo sapiens (human);RNA polymerase - Homo sapiens (human);Purine metabolism - Homo sapiens (human);Epstein-Barr virus infection - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;Pyrimidine metabolism;Eukaryotic Transcription Initiation;FGFR2 alternative splicing;Signaling by FGFR2;DNA Repair;Disease;RNA Pol II CTD phosphorylation and interaction with CE during HIV infection;Signal Transduction;Formation of the HIV-1 Early Elongation Complex;Gene expression (Transcription);Signaling by FGFR;Formation of HIV-1 elongation complex containing HIV-1 Tat;Tat-mediated elongation of the HIV-1 transcript;Abortive elongation of HIV-1 transcript in the absence of Tat;HIV Transcription Elongation;HIV elongation arrest and recovery;Formation of HIV elongation complex in the absence of HIV Tat;Pausing and recovery of HIV elongation;Generic Transcription Pathway;Tat-mediated HIV elongation arrest and recovery;Pausing and recovery of Tat-mediated HIV elongation;Transcription of the HIV genome;Late Phase of HIV Life Cycle;HIV Life Cycle;HIV Infection;RNA Polymerase II HIV Promoter Escape;RNA Polymerase II Pre-transcription Events;RNA Polymerase II Transcription Initiation;RNA Polymerase II Transcription Initiation And Promoter Clearance;RNA Pol II CTD phosphorylation and interaction with CE;Viral Messenger RNA Synthesis;Influenza Viral RNA Transcription and Replication;Formation of RNA Pol II elongation complex ;Influenza Life Cycle;Influenza Infection;HIV Transcription Initiation;RNA polymerase II transcribes snRNA genes;RNA Polymerase II Transcription;Metabolism of RNA;Infectious disease;Purine metabolism;RNA Polymerase II Transcription Elongation;mRNA Splicing - Major Pathway;Pyrimidine metabolism;RNA Polymerase II Promoter Escape;RNA Polymerase II Transcription Pre-Initiation And Promoter Opening;TP53 Regulates Transcription of DNA Repair Genes;Signaling by Nuclear Receptors;Transcriptional Regulation by TP53;mRNA Capping;Formation of the Early Elongation Complex;Estrogen-dependent gene expression;Transcriptional regulation by small RNAs;Signaling by Receptor Tyrosine Kinases;ESR-mediated signaling;Formation of TC-NER Pre-Incision Complex;mRNA Splicing - Minor Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA;Dual incision in TC-NER;Gap-filling DNA repair synthesis and ligation in TC-NER;Transcription-Coupled Nucleotide Excision Repair (TC-NER);Nucleotide Excision Repair;Gene Silencing by RNA (Consensus)

Recessive Scores

• pRec: 0.240

Intolerance Scores

• loftool: 0.311
• rvis_EVS: -0.18
• rvis_percentile_EVS: 39.95

Haploinsufficiency Scores

• pHI: 0.448
• hipred: Y
• hipred_score: 0.693
• ghis: 0.569

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.701

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Polr2c

Gene ontology

• Biological process: mRNA splicing, via spliceosome;transcription-coupled nucleotide-excision repair;transcription by RNA polymerase II;transcription initiation from RNA polymerase II promoter;transcription elongation from RNA polymerase II promoter;7-methylguanosine mRNA capping;fibroblast growth factor receptor signaling pathway;RNA metabolic process;snRNA transcription by RNA polymerase II;regulation of gene silencing by miRNA
• Cellular component: nucleus;nucleoplasm;RNA polymerase II, core complex;cytosol;microtubule cytoskeleton
• Molecular function: RNA polymerase II activity;DNA binding;protein binding;protein dimerization activity