CPSF4
Basic information
Region (hg38): 7:99438922-99457373
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPSF4 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 | |||||
| missense | 1 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 1 | 0 | 1 |
Variants in CPSF4
This is a list of pathogenic ClinVar variants found in the CPSF4 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 7-99450755-G-A | not specified | Uncertain significance (Nov 20, 2024) | ||
| 7-99450756-T-C | not specified | Uncertain significance (Feb 28, 2023) | ||
| 7-99450781-G-A | Benign (Jan 15, 2018) | |||
| 7-99452415-C-T | not specified | Uncertain significance (Aug 28, 2024) | ||
| 7-99452438-A-C | not specified | Uncertain significance (Sep 24, 2024) | ||
| 7-99454111-C-A | not specified | Uncertain significance (Oct 08, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CPSF4 | protein_coding | protein_coding | ENST00000292476 | 8 | 18450 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.268 | 0.731 | 125733 | 0 | 15 | 125748 | 0.0000596 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.29 | 51 | 172 | 0.296 | 0.0000105 | 1786 |
| Missense in Polyphen | 4 | 48.623 | 0.082265 | 544 | ||
| Synonymous | -0.489 | 75 | 69.8 | 1.07 | 0.00000463 | 484 |
| Loss of Function | 2.85 | 4 | 16.5 | 0.242 | 7.67e-7 | 191 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000905 | 0.0000904 |
| Ashkenazi Jewish | 0.000401 | 0.000397 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000441 | 0.0000439 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000133 | 0.000131 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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. CPSF4 binds RNA polymers with a preference for poly(U). {ECO:0000269|PubMed:14749727, ECO:0000269|PubMed:9224719}.;
- Pathway
- Influenza A - Homo sapiens (human);mRNA surveillance pathway - Homo sapiens (human);mRNA Processing;tRNA processing;Disease;Gene expression (Transcription);polyadenylation of mrna;NS1 Mediated Effects on Host Pathways;Host Interactions with Influenza Factors;Influenza Infection;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;Infectious disease;mRNA Splicing - Major Pathway;Transport of Mature mRNA Derived from an Intronless Transcript;Transport of Mature mRNAs Derived from Intronless Transcripts;tRNA processing in the nucleus;Inhibition of Host mRNA Processing and RNA Silencing;mRNA Splicing;mRNA 3,-end processing;Transport of Mature Transcript to Cytoplasm;Processing of Capped Intron-Containing Pre-mRNA
(Consensus)
Recessive Scores
- pRec
- 0.171
Intolerance Scores
- loftool
- 0.554
- rvis_EVS
- -0.16
- rvis_percentile_EVS
- 41.25
Haploinsufficiency Scores
- pHI
- 0.315
- hipred
- Y
- hipred_score
- 0.696
- ghis
- 0.545
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- K
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.879
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cpsf4
- Phenotype
Zebrafish Information Network
- Gene name
- cpsf4
- Affected structure
- pharyngeal arch 1
- Phenotype tag
- abnormal
- Phenotype quality
- malformed
Gene ontology
- Biological process
- mRNA splicing, via spliceosome;termination of RNA polymerase II transcription;mRNA export from nucleus;mRNA 3'-end processing;modification by virus of host mRNA processing;pre-mRNA cleavage required for polyadenylation
- Cellular component
- nucleoplasm;mRNA cleavage and polyadenylation specificity factor complex;intracellular membrane-bounded organelle
- Molecular function
- RNA binding;protein binding;zinc ion binding