GeneBe

CPSF1

protein-coding

cleavage and polyadenylation specific factor 1, the group of Cleavage and polyadenylation specific factor subunits|MicroRNA protein coding host genes

Gene summary

Cleavage and polyadenylation specificity factor (CPSF) is a multisubunit complex that plays a central role in 3-prime processing of pre-mRNAs. CPSF recognizes the AAUAAA signal in the pre-mRNA and interacts with other proteins to facilitate both RNA cleavage and poly(A) synthesis. CPSF1 is the largest subunit of the CPSF complex (Murthy and Manley, 1995 [PubMed 7590244]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_013291.3

Inheritance

AD

ClinVar variants

P:9U:270B:45

Top phenotype

Myopia 27, autosomal dominant

gnomAD constraint

pLI —, LoF o/e 0.4

Max pathogenic AF

—

Genomic locus

chr8:144,393,229-144,409,335

External References & Databases

Ensembl (ENSG00000071894)NCBI Gene (29894)OMIM (606027)HGNC:2324GenCCUniProt (Q10570)AlphaFoldClinVar (CPSF1)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~16.1 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

myopia 27STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0032941

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Myopia 27, autosomal dominantAD

Manifestation: Ophthalmologic

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 30689892Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CPSF1 variants in ClinVar

4 Conditions Cataloged
not specifiedTotal: 246
CPSF1-related disorderTotal: 30
not providedTotal: 28
Myopia 27Total: 18

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_013291.3. 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.

EffectPLPVUSLBBSum
synonymous
6
clinvar
37
clinvar
1
clinvar
 44
missense
1
clinvar
239
clinvar
5
clinvar
 245
nonsense
1
clinvar
2
clinvar
 3
start loss
0
frameshift
2
clinvar
3
clinvar
2
clinvar
2
clinvar
 9
splice donor/acceptor (+/-2bp)
1
clinvar
1
clinvar
21
clinvar
 23
Total54270441324

Highest pathogenic variant AF is 0.00008061356

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 56 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_013291.3RefSeqNP_037423.237MANE Select
ENST00000616140.2EnsemblENSP00000484669.137MANE Select
ENST00000531042.5EnsemblENSP00000435761.25Standard
ENST00000531727.5EnsemblENSP00000483775.16Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
cpsf1Danio rerio

Structure: hematopoietic stem cell

Quality: decreased amount

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • mRNA surveillance pathway - Homo sapiens (human)
  • mRNA Processing
  • tRNA processing
  • Gene expression (Transcription)
  • polyadenylation of mrna

Biological Process

  • mRNA splicing, via spliceosome
  • termination of RNA polymerase II transcription
  • mRNA polyadenylation
  • mRNA export from nucleus
  • mRNA 3'-end processing

Molecular Function

  • protein binding
  • enzyme binding
  • mRNA 3'-UTR AU-rich region binding

Cellular Component

  • nucleus
  • nucleoplasm
  • mRNA cleavage and polyadenylation specificity factor complex

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000349769
Coding exons
37
Length
16310
Individuals with no LoFs
125565
Homozygous LoFs
0
Heterozygous LoFs
172
Defined
125737
p
0.000684
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense2.807199640.7460.00006689325
Missense (PolyPhen)173333.370.518953253
Synonymous-3.055084281.190.00003322919
Loss of Function4.843075.30.3980.00000365822

Population LoF Frequency

PopulationCAFp-valueStatus
African0.00390.0026notable
Latino/Admixed American0.000760.00055rare
Ashkenazi Jewish0.00250.0016notable
East Asian0.000500.00049rare
Finnish0.0000480.000046rare
European (Non-Finnish)0.000810.00060rare
South Asian0.000430.00042rare
Other0.000840.00049rare

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Component of the cleavage and polyadenylation specificity factor (CPSF) complex that plays 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. This subunit is involved in the RNA recognition step of the polyadenylation reaction. {ECO:0000269|PubMed:14749727}.;

Recessive Scores

pRec
0.131

Intolerance Scores

LoFtool
0.668
RVIS EVS
-3.4
RVIS percentile EVS
0.37

Essentials

Essential (CRISPR)
E
Essential (CRISPR2)
E
Essential (gene trap)
H
Indispensability pred.
E
Indispensability score
0.911

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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