POLR1F

RNA polymerase I subunit F, the group of MicroRNA protein coding host genes|RNA polymerase subunits

Basic information

Region (hg38): 7:19695461-19709037

Previous symbols: [ "TWISTNB" ]

Links

ENSG00000105849 ∙ NCBI:221830 ∙ OMIM:608312 ∙ HGNC:18027 ∙ Uniprot:Q3B726 ∙ 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 POLR1F gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the POLR1F 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			25	4		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	4	0

Variants in POLR1F

This is a list of pathogenic ClinVar variants found in the POLR1F region.

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

Position	Type	Phenotype	Significance	ClinVar
7-19698348-G-T		not specified	Uncertain significance (Mar 12, 2024)
7-19698353-C-T		not specified	Uncertain significance (Dec 19, 2023)
7-19698357-T-C		not specified	Likely benign (Apr 23, 2024)
7-19698377-G-A		not specified	Uncertain significance (Dec 28, 2024)
7-19698390-G-T		not specified	Uncertain significance (Jul 26, 2022)
7-19698455-A-T		not specified	Uncertain significance (Dec 04, 2024)
7-19698533-G-A		not specified	Likely benign (Apr 19, 2024)
7-19698587-T-C		not specified	Uncertain significance (Mar 07, 2025)
7-19698680-C-T		not specified	Uncertain significance (Dec 31, 2024)
7-19698686-T-C		not specified	Uncertain significance (May 08, 2023)
7-19698713-C-G		not specified	Uncertain significance (Jun 12, 2023)
7-19698713-C-T		not specified	Uncertain significance (May 26, 2024)
7-19700093-C-T		not specified	Uncertain significance (Apr 09, 2024)
7-19700101-G-C		not specified	Uncertain significance (Jun 26, 2024)
7-19700130-G-A		not specified	Uncertain significance (Feb 09, 2025)
7-19700170-C-T		not specified	Uncertain significance (Aug 19, 2024)
7-19700204-G-A		not specified	Uncertain significance (Jun 25, 2024)
7-19700231-C-A		not specified	Uncertain significance (Mar 21, 2022)
7-19700232-C-G		not specified	Uncertain significance (Nov 29, 2023)
7-19704785-C-G		not specified	Uncertain significance (Oct 29, 2024)
7-19704795-G-T		not specified	Uncertain significance (May 03, 2023)
7-19704796-G-C		not specified	Uncertain significance (Aug 07, 2024)
7-19704811-T-G		not specified	Uncertain significance (Jan 23, 2025)
7-19704837-T-C		not specified	Uncertain significance (Dec 06, 2024)
7-19704883-C-A		not specified	Uncertain significance (Feb 08, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
POLR1F	protein_coding	protein_coding	ENST00000222567	4	13626

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.617	0.381	125741	0	7	125748	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.157	174	180	0.967	0.00000842	2214
Missense in Polyphen		48	61.126	0.78526		753
Synonymous	0.220	67	69.3	0.966	0.00000330	643
Loss of Function	2.62	2	11.7	0.172	4.94e-7	159

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000894	0.0000894
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.00000880	0.00000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000338	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 I which synthesizes ribosomal RNA precursors. Through its association with RRN3/TIF-IA may be involved in recruitment of Pol I to rDNA promoters.
• Pathway: Pyrimidine metabolism - Homo sapiens (human);RNA polymerase - Homo sapiens (human);Purine metabolism - Homo sapiens (human);Pyrimidine metabolism;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;RNA Polymerase I Transcription Termination;RNA Polymerase I Transcription;RNA Polymerase I Transcription Initiation;RNA Polymerase I Promoter Escape;RNA Polymerase I Chain Elongation (Consensus)

Recessive Scores

• pRec: 0.126

Intolerance Scores

• loftool: 0.203
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.53

Haploinsufficiency Scores

• pHI: 0.143
• hipred: Y
• hipred_score: 0.577
• ghis: 0.612

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.872

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Twistnb

Zebrafish Information Network

• Gene name: twistnb
• Affected structure: trunk
• Phenotype tag: abnormal
• Phenotype quality: curved ventral

Gene ontology

• Biological process: transcription initiation from RNA polymerase I promoter;termination of RNA polymerase I transcription;positive regulation of gene expression, epigenetic;cellular response to leukemia inhibitory factor
• Cellular component: nucleoplasm;RNA polymerase I complex
• Molecular function: RNA polymerase I activity;DNA-directed 5'-3' RNA polymerase activity