POLR2D

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

Basic information

Region (hg38): 2:127843553-127858155

Links

ENSG00000144231

∙ NCBI:5433 ∙ OMIM:606017 ∙ HGNC:9191 ∙ Uniprot:O15514 ∙ 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 POLR2D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the POLR2D 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			7 clinvar			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in POLR2D

This is a list of pathogenic ClinVar variants found in the POLR2D region.

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

Position	Phenotype	Significance	ClinVar
2-127848124-G-A	not specified	Uncertain significance (Nov 08, 2024)	3422791
2-127850609-A-C	not specified	Uncertain significance (Dec 14, 2022)	2361070
2-127850683-A-G	not specified	Uncertain significance (Dec 03, 2021)	2264234
2-127858078-G-A	not specified	Uncertain significance (Nov 07, 2023)	3216529
2-127858078-G-C	not specified	Uncertain significance (Aug 02, 2021)	2240679
2-127858081-T-A	not specified	Uncertain significance (Dec 19, 2022)	2336729
2-127858088-C-T	not specified	Uncertain significance (Mar 19, 2024)	3308810

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
POLR2D	protein_coding	protein_coding	ENST00000272645	4	11892

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.214	0.751	125739	0	4	125743	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.58	39	78.4	0.497	0.00000433	933
Missense in Polyphen		7	22.179	0.31562		247
Synonymous	0.434	23	25.8	0.891	0.00000123	247
Loss of Function	1.75	2	7.01	0.285	3.61e-7	89

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000310	0.0000310
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000268	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
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. RPB4 is part of a subcomplex with RPB7 that binds to a pocket formed by RPB1, RPB2 and RPB6 at the base of the clamp element. The RBP4-RPB7 subcomplex seems to lock the clamp via RPB7 in the closed conformation thus preventing double-stranded DNA to enter the active site cleft. The RPB4-RPB7 subcomplex binds single-stranded DNA and RNA (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);Pyrimidine metabolism;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: 0.208

Intolerance Scores

loftool: 0.469
rvis_EVS: -0.12
rvis_percentile_EVS: 44.54

Haploinsufficiency Scores

pHI: 0.475
hipred: Y
hipred_score: 0.705
ghis: 0.696

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: E
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.940

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Polr2d
Phenotype

Zebrafish Information Network

Gene name: polr2d
Affected structure: head
Phenotype tag: abnormal
Phenotype quality: flat

Gene ontology

Biological process: nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay;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;mRNA export from nucleus in response to heat stress;recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex;snRNA transcription by RNA polymerase II;positive regulation of translational initiation;regulation of gene silencing by miRNA
Cellular component: P-body;nucleus;nucleoplasm;RNA polymerase II, core complex;cytosol;nuclear speck
Molecular function: nucleotide binding;single-stranded DNA binding;single-stranded RNA binding;DNA-directed 5'-3' RNA polymerase activity;translation initiation factor binding