CPSF2

cleavage and polyadenylation specific factor 2, the group of Cleavage and polyadenylation specific factor subunits|MBL fold containing DNA/RNA interacting subfamily

Basic information

Region (hg38): 14:92121969-92172145

Links

ENSG00000165934

∙ NCBI:53981 ∙ OMIM:606028 ∙ HGNC:2325 ∙ Uniprot:Q9P2I0 ∙ 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 CPSF2 gene.

not_specified (52 variants)
not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPSF2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000017437.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	2 clinvar		5
missense			55 clinvar			55
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	59	2	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CPSF2	protein_coding	protein_coding	ENST00000298875	14	42475

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.13e-8	0.998	125685	0	63	125748	0.000251

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.34	222	413	0.538	0.0000204	5169
Missense in Polyphen		57	160.22	0.35576		1999
Synonymous	0.632	132	142	0.932	0.00000685	1450
Loss of Function	2.78	18	36.0	0.499	0.00000175	486

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000338	0.000336
Ashkenazi Jewish	0.00110	0.00109
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000275	0.000273
Middle Eastern	0.000163	0.000163
South Asian	0.000262	0.000261
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

Function: FUNCTION: Component of the cleavage and polyadenylation specificity factor (CPSF) complex that play a key role in pre-mRNA 3'-end formation, recognizing the AAUAAA signal sequence and interacting with poly(A) polymerase and other factors to bring about cleavage and poly(A) addition. Involved in the histone 3' end pre-mRNA processing. {ECO:0000269|PubMed:14749727, ECO:0000269|PubMed:18688255}.;
Pathway: mRNA surveillance pathway - Homo sapiens (human);mRNA Processing;Gene expression (Transcription);polyadenylation of mrna;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;Transport of Mature mRNA Derived from an Intronless Transcript;Transport of Mature mRNAs Derived from Intronless Transcripts;mRNA Splicing;mRNA 3,-end processing;Transport of Mature Transcript to Cytoplasm;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

pRec: 0.148

Intolerance Scores

loftool: 0.735
rvis_EVS: -0.67
rvis_percentile_EVS: 15.76

Haploinsufficiency Scores

pHI: 0.186
hipred: Y
hipred_score: 0.637
ghis: 0.678

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: E
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.972

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Cpsf2
Phenotype

Gene ontology

Biological process: mRNA splicing, via spliceosome;termination of RNA polymerase II transcription;mRNA polyadenylation;mRNA cleavage;mRNA 3'-end processing by stem-loop binding and cleavage;mRNA export from nucleus;mRNA 3'-end processing
Cellular component: nucleoplasm;mRNA cleavage and polyadenylation specificity factor complex;membrane
Molecular function: RNA binding;protein binding