PCF11

protein-coding

PCF11 cleavage and polyadenylation factor subunit

Gene summary

The protein encoded by this gene binds to CLP1 to form pre-mRNA cleavage factor IIm. The encoded protein is necessary for efficient Pol II transcription termination and may be involved in degradation of the 3' product of polyA site cleavage. [provided by RefSeq, Oct 2016]

MANE transcript

NM_001346413.3

Inheritance

—

ClinVar variants

U:170B:9

Top phenotype

Mediastinal germ cell tumor

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr11:83,156,988-83,187,451

External References & Databases

Ensembl (ENSG00000165494)

Transcript & Mutation Effects

hg38 • Region Span ~30.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PCF11 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 163

not providedTotal: 5

Mediastinal germ cell tumorTotal: 1

Acute megakaryoblastic leukemiaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001346413.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar	2 clinvar	4
missense			167 clinvar	3 clinvar	2 clinvar	172
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	170	5	4	179

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 14 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001346413.3	RefSeq	NP_001333342.1	16	MANE Select
ENST00000690938.1	Ensembl	ENSP00000508500.1	16	MANE Select
NM_001346414.2	RefSeq	NP_001333343.1	16	Standard
NM_001346415.2	RefSeq	NP_001333344.1	16	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

mRNA surveillance pathway - Homo sapiens (human)
Gene expression (Transcription)
RNA Polymerase II Transcription
Metabolism of RNA
Processing of Intronless Pre-mRNAs

Biological Process

mRNA splicing, via spliceosome
termination of RNA polymerase II transcription
mRNA polyadenylation
mRNA cleavage
mRNA 3'-end processing

Molecular Function

RNA polymerase II complex binding
mRNA binding

Cellular Component

nucleoplasm
cytoplasm
mitochondrion
mRNA cleavage factor complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000298281
Coding exons: 16
Length: 30464
Individuals with no LoFs: 124625
Homozygous LoFs: 0
Heterozygous LoFs: 3
Defined: 124628
p: 0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.66	574	783	0.733	0.0000391	10106
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.000056	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Component of pre-mRNA cleavage complex II.;

Recessive Scores

pRec: 0.114

Intolerance Scores

LoFtool: 0.114
RVIS EVS: -0.21
RVIS percentile EVS: 37.75

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.937

Gene Damage Prediction

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