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.

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.

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			29			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	29	0	0

Variants in CPSF2

This is a list of pathogenic ClinVar variants found in the CPSF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-92131012-C-G		not specified	Uncertain significance (Sep 27, 2021)
14-92131108-A-G		not specified	Uncertain significance (May 27, 2022)
14-92134343-G-A		not specified	Uncertain significance (Jun 10, 2024)
14-92135367-G-A		not specified	Uncertain significance (Dec 03, 2021)
14-92135387-A-G		not specified	Uncertain significance (Feb 05, 2024)
14-92142170-T-C		not specified	Uncertain significance (Oct 05, 2023)
14-92142302-C-T		not specified	Uncertain significance (Nov 21, 2023)
14-92143004-G-A		not specified	Uncertain significance (Jun 22, 2023)
14-92143140-G-A		not specified	Uncertain significance (Oct 02, 2023)
14-92143151-C-A		not specified	Uncertain significance (Aug 09, 2021)
14-92143173-A-C		not specified	Uncertain significance (Jul 05, 2023)
14-92143235-C-T		not specified	Uncertain significance (Feb 28, 2024)
14-92143245-T-C		not specified	Uncertain significance (Aug 26, 2022)
14-92143250-C-T		not specified	Uncertain significance (Mar 01, 2024)
14-92143251-G-A		not specified	Uncertain significance (Jan 09, 2024)
14-92155191-C-T		not specified	Uncertain significance (Jun 03, 2022)
14-92155227-G-A		not specified	Uncertain significance (Dec 21, 2022)
14-92155259-T-G		not specified	Uncertain significance (Jun 10, 2024)
14-92155268-A-T		not specified	Uncertain significance (Dec 27, 2022)
14-92156567-A-G		not specified	Uncertain significance (Jan 20, 2023)
14-92156626-A-C		not specified	Uncertain significance (Jan 31, 2023)
14-92157664-G-A		not specified	Uncertain significance (Jul 27, 2021)
14-92157799-G-A		not specified	Uncertain significance (Jan 26, 2023)
14-92159056-A-T		not specified	Uncertain significance (May 24, 2023)
14-92159083-A-C		not specified	Uncertain significance (Mar 29, 2023)

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

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