CSTF3

cleavage stimulation factor subunit 3, the group of Cleavage stimulation factor subunits

Basic information

Region (hg38): 11:33077188-33162371

Links

ENSG00000176102 ∙ NCBI:1479 ∙ OMIM:600367 ∙ HGNC:2485 ∙ Uniprot:Q12996 ∙ 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 CSTF3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CSTF3 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			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	0	0

Variants in CSTF3

This is a list of pathogenic ClinVar variants found in the CSTF3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-33085143-C-T		not specified	Uncertain significance (Feb 14, 2023)
11-33085191-C-T		not specified	Uncertain significance (Nov 18, 2023)
11-33085223-G-A		not specified	Uncertain significance (Feb 28, 2023)
11-33085733-C-T		not specified	Uncertain significance (Jan 24, 2023)
11-33085902-C-T		not specified	Uncertain significance (Dec 16, 2021)
11-33087024-G-C		not specified	Uncertain significance (Nov 14, 2023)
11-33087084-T-C		not specified	Uncertain significance (Jun 24, 2022)
11-33087098-A-G		not specified	Uncertain significance (Dec 08, 2023)
11-33087131-C-G		not specified	Uncertain significance (Apr 07, 2023)
11-33090671-A-C		not specified	Uncertain significance (Feb 11, 2022)
11-33096365-T-G		not specified	Uncertain significance (Dec 28, 2022)
11-33096866-G-C		not specified	Uncertain significance (Jun 06, 2023)
11-33107982-T-A		not specified	Uncertain significance (Sep 22, 2023)
11-33141716-G-A		not specified	Uncertain significance (Nov 15, 2021)
11-33141741-G-A		not specified	Uncertain significance (Feb 02, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CSTF3	protein_coding	protein_coding	ENST00000323959	21	85184

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.983	0.0172	125729	0	17	125746	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.94	113	386	0.293	0.0000206	4710
Missense in Polyphen		15	78.08	0.19211		896
Synonymous	1.43	104	124	0.836	0.00000625	1286
Loss of Function	5.32	8	47.6	0.168	0.00000287	568

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000217	0.000217
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000721	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.0000807	0.0000653
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.
• 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;mRNA 3,-end processing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.163

Intolerance Scores

• loftool: 0.596
• rvis_EVS: -0.63
• rvis_percentile_EVS: 17.03

Haploinsufficiency Scores

• pHI: 0.631
• hipred: Y
• hipred_score: 0.651
• ghis: 0.674

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.985

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cstf3

Zebrafish Information Network

• Gene name: cstf3
• Affected structure: anatomical system
• Phenotype tag: abnormal
• Phenotype quality: quality

Gene ontology

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