CSTF1

cleavage stimulation factor subunit 1, the group of Cleavage stimulation factor subunits|WD repeat domain containing

Basic information

Region (hg38): 20:56392370-56406362

Links

ENSG00000101138 ∙ NCBI:1477 ∙ OMIM:600369 ∙ HGNC:2483 ∙ Uniprot:Q05048 ∙ 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 CSTF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CSTF1 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in CSTF1

This is a list of pathogenic ClinVar variants found in the CSTF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-56395634-A-G		not specified	Uncertain significance (Dec 20, 2023)
20-56395638-G-A		not specified	Uncertain significance (Nov 15, 2021)
20-56395647-A-G		not specified	Uncertain significance (Mar 03, 2022)
20-56395659-A-G		not specified	Uncertain significance (Sep 20, 2023)
20-56395666-C-G		not specified	Uncertain significance (Jun 24, 2022)
20-56398982-C-T		not specified	Uncertain significance (May 04, 2023)
20-56399081-T-C		not specified	Uncertain significance (Aug 06, 2021)
20-56399181-A-G		not specified	Uncertain significance (Jan 24, 2024)
20-56399189-G-A		not specified	Uncertain significance (Jul 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CSTF1	protein_coding	protein_coding	ENST00000217109	5	12092

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.954	0.0460	125741	0	3	125744	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.41	110	267	0.413	0.0000161	2830
Missense in Polyphen		17	62.686	0.27119		630
Synonymous	-1.46	123	104	1.18	0.00000698	844
Loss of Function	3.55	2	18.5	0.108	0.00000102	210

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000547	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.0000547	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: One of the multiple factors required for polyadenylation and 3'-end cleavage of mammalian pre-mRNAs. May be responsible for the interaction of CSTF with other factors to form a stable complex on the pre-mRNA.
• 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;mRNA Splicing;BARD1 signaling events;mRNA 3,-end processing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.171
• rvis_EVS: -0.71
• rvis_percentile_EVS: 14.4

Haploinsufficiency Scores

• pHI: 0.293
• hipred: Y
• hipred_score: 0.825
• ghis: 0.704

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.996

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cstf1

Gene ontology

• Biological process: mRNA splicing, via spliceosome;termination of RNA polymerase II transcription;mRNA 3'-end processing
• Cellular component: nucleoplasm;mRNA cleavage stimulating factor complex
• Molecular function: RNA binding;protein binding