PCF11

PCF11 cleavage and polyadenylation factor subunit

Basic information

Region (hg38): 11:83156987-83187451

Links

ENSG00000165494 ∙ NCBI:51585 ∙ OMIM:608876 ∙ HGNC:30097 ∙ Uniprot:O94913 ∙ 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 PCF11 gene.

• Inborn genetic diseases (35 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCF11 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				1	2	3
missense			35		2	37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	35	1	4

Variants in PCF11

This is a list of pathogenic ClinVar variants found in the PCF11 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-83157508-G-T		not specified	Uncertain significance (Aug 08, 2022)
11-83163805-C-T		not specified	Uncertain significance (Dec 20, 2023)
11-83164259-C-G		not specified	Uncertain significance (Jan 03, 2022)
11-83165623-G-C		not specified	Uncertain significance (Jan 03, 2024)
11-83165658-C-T		not specified	Uncertain significance (Jul 11, 2023)
11-83165679-T-C		not specified	Uncertain significance (Apr 04, 2023)
11-83165703-C-T		not specified	Uncertain significance (Jan 16, 2024)
11-83165738-C-T		not specified	Uncertain significance (Dec 08, 2021)
11-83165744-C-T		not specified	Uncertain significance (Apr 25, 2023)
11-83165988-C-T		not specified	Uncertain significance (Jan 10, 2023)
11-83166083-G-C		not specified	Uncertain significance (Jan 11, 2023)
11-83166088-G-A		not specified	Uncertain significance (Nov 17, 2023)
11-83166192-A-G		not specified	Uncertain significance (Dec 30, 2023)
11-83166200-A-G		not specified	Uncertain significance (Nov 03, 2022)
11-83166210-C-T		not specified	Uncertain significance (Feb 03, 2022)
11-83166275-A-G		not specified	Uncertain significance (Dec 07, 2021)
11-83166297-A-G		not specified	Uncertain significance (Feb 23, 2023)
11-83166356-T-C		not specified	Uncertain significance (Oct 18, 2021)
11-83166434-A-G		not specified	Uncertain significance (Feb 28, 2024)
11-83166506-C-T		not specified	Uncertain significance (Nov 08, 2021)
11-83166528-C-T		not specified	Uncertain significance (Sep 20, 2023)
11-83166554-C-T		not specified	Uncertain significance (Jun 22, 2021)
11-83166591-G-A		not specified	Uncertain significance (Jan 16, 2024)
11-83166596-C-G		not specified	Uncertain significance (Dec 08, 2023)
11-83166608-A-T		not specified	Uncertain significance (Dec 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCF11	protein_coding	protein_coding	ENST00000298281	16	30464

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	1.39e-12	124625	0	3	124628	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.66	574	783	0.733	0.0000391	10106
Missense in Polyphen		130	264.36	0.49176		3521
Synonymous	-1.21	298	273	1.09	0.0000133	3026
Loss of Function	8.00	0	74.6	0.00	0.00000465	862

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000178	0.0000177
Middle Eastern	0.000111	0.0000556
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of pre-mRNA cleavage complex II.
• Pathway: mRNA surveillance pathway - Homo sapiens (human);Gene expression (Transcription);RNA Polymerase II Transcription;Metabolism of RNA;Processing of Intronless Pre-mRNAs;Processing of Capped Intronless Pre-mRNA;Cleavage of Growing Transcript in the Termination Region ;RNA Polymerase II Transcription Termination;mRNA Splicing - Major Pathway;mRNA Splicing;mRNA 3,-end processing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.114
• rvis_EVS: -0.21
• rvis_percentile_EVS: 37.75

Haploinsufficiency Scores

• pHI: 0.618
• hipred: Y
• hipred_score: 0.783
• ghis: 0.554

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.937

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcf11

Gene ontology

• Biological process: mRNA splicing, via spliceosome;termination of RNA polymerase II transcription;mRNA polyadenylation;mRNA cleavage;mRNA 3'-end processing
• Cellular component: nucleoplasm;cytoplasm;mitochondrion;mRNA cleavage factor complex
• Molecular function: RNA polymerase II complex binding;mRNA binding