CPSF7

cleavage and polyadenylation specific factor 7, the group of RNA binding motif containing|Cleavage factor Im complex subunits

Basic information

Region (hg38): 11:61402641-61430031

Links

ENSG00000149532 ∙ NCBI:79869 ∙ ∙ HGNC:30098 ∙ Uniprot:Q8N684 ∙ 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 CPSF7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPSF7 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			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	0

Variants in CPSF7

This is a list of pathogenic ClinVar variants found in the CPSF7 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-61410968-T-A		not specified	Uncertain significance (Nov 13, 2024)
11-61411810-T-G		not specified	Uncertain significance (Sep 28, 2021)
11-61416159-C-G		not specified	Uncertain significance (Nov 13, 2024)
11-61416277-G-T		not specified	Uncertain significance (Aug 05, 2024)
11-61416333-G-A		not specified	Uncertain significance (Jan 23, 2023)
11-61416376-G-T		not specified	Uncertain significance (Dec 06, 2024)
11-61416430-G-A		not specified	Uncertain significance (Oct 12, 2022)
11-61416447-A-G		not specified	Uncertain significance (Sep 01, 2021)
11-61416449-G-T		not specified	Uncertain significance (Dec 07, 2021)
11-61419946-C-CA		Malignant tumor of prostate	Uncertain significance (-)
11-61420021-T-G		not specified	Uncertain significance (Apr 20, 2023)
11-61420042-G-A		not specified	Uncertain significance (Apr 19, 2024)
11-61420534-T-C		not specified	Uncertain significance (Nov 13, 2023)
11-61421431-G-A		not specified	Uncertain significance (Apr 07, 2023)
11-61421442-T-C		not specified	Uncertain significance (Jan 31, 2024)
11-61421463-G-T		not specified	Uncertain significance (Dec 14, 2023)
11-61421496-C-T		not specified	Uncertain significance (Feb 10, 2022)
11-61421525-G-C		not specified	Uncertain significance (Nov 27, 2024)
11-61429764-G-A		not specified	Uncertain significance (May 09, 2024)
11-61429790-G-A		not specified	Uncertain significance (Nov 23, 2024)
11-61429791-G-C		not specified	Uncertain significance (Nov 15, 2021)
11-61429797-G-A		not specified	Uncertain significance (Aug 05, 2024)
11-61429988-GC-G			Benign (Jun 23, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CPSF7	protein_coding	protein_coding	ENST00000340437	9	27383

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.00127	125733	0	2	125735	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.59	187	317	0.591	0.0000189	3309
Missense in Polyphen		66	135.84	0.48586		1360
Synonymous	1.46	94	114	0.826	0.00000595	1115
Loss of Function	4.33	1	23.8	0.0420	0.00000157	240

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000616	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the cleavage factor Im (CFIm) complex that functions as an activator of the pre-mRNA 3'-end cleavage and polyadenylation processing required for the maturation of pre-mRNA into functional mRNAs (PubMed:8626397, PubMed:17024186, PubMed:29276085). CFIm contributes to the recruitment of multiprotein complexes on specific sequences on the pre-mRNA 3'- end, so called cleavage and polyadenylation signals (pA signals) (PubMed:8626397, PubMed:17024186). Most pre-mRNAs contain multiple pA signals, resulting in alternative cleavage and polyadenylation (APA) producing mRNAs with variable 3'-end formation (PubMed:23187700, PubMed:29276085). The CFIm complex acts as a key regulator of cleavage and polyadenylation site choice during APA through its binding to 5'-UGUA-3' elements localized in the 3'- untranslated region (UTR) for a huge number of pre-mRNAs (PubMed:20695905, PubMed:29276085). CPSF7 activates directly the mRNA 3'-processing machinery (PubMed:29276085). Binds to pA signals in RNA substrates (PubMed:8626397, PubMed:17024186). {ECO:0000269|PubMed:17024186, ECO:0000269|PubMed:20695905, ECO:0000269|PubMed:23187700, ECO:0000269|PubMed:29276085, ECO:0000269|PubMed:8626397}.
• 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)

Intolerance Scores

• loftool: 0.0256
• rvis_EVS: -0.63
• rvis_percentile_EVS: 17.03

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.793
• ghis: 0.602

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.910

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cpsf7

Gene ontology

• Biological process: mRNA splicing, via spliceosome;termination of RNA polymerase II transcription;mRNA 3'-end processing;protein tetramerization;protein heterotetramerization;pre-mRNA cleavage required for polyadenylation;mRNA alternative polyadenylation;messenger ribonucleoprotein complex assembly
• Cellular component: nucleus;nucleoplasm;cytoplasm;mRNA cleavage and polyadenylation specificity factor complex;mRNA cleavage factor complex;membrane
• Molecular function: RNA binding;protein binding