CSTF2T

cleavage stimulation factor subunit 2 tau variant, the group of RNA binding motif containing|Cleavage stimulation factor subunits

Basic information

Region (hg38): 10:51695485-51699595

Links

ENSG00000177613 ∙ NCBI:23283 ∙ OMIM:611968 ∙ HGNC:17086 ∙ Uniprot:Q9H0L4 ∙ 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 CSTF2T gene.

• Inborn genetic diseases (21 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CSTF2T 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			20	1	1	22
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	2	1

Variants in CSTF2T

This is a list of pathogenic ClinVar variants found in the CSTF2T region.

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

Position	Type	Phenotype	Significance	ClinVar
10-51697728-G-T		not specified	Uncertain significance (May 08, 2023)
10-51697771-C-A		not specified	Uncertain significance (Jan 23, 2024)
10-51697829-T-C		not specified	Uncertain significance (Jan 04, 2024)
10-51697833-C-G		not specified	Uncertain significance (Mar 11, 2024)
10-51697834-C-G		not specified	Uncertain significance (Dec 21, 2023)
10-51697836-G-C		not specified	Uncertain significance (Mar 22, 2023)
10-51697902-C-G		not specified	Uncertain significance (Jun 06, 2023)
10-51697910-C-A		not specified	Uncertain significance (Oct 05, 2023)
10-51697926-C-T		not specified	Uncertain significance (Nov 06, 2023)
10-51697928-C-A		not specified	Likely benign (Nov 06, 2023)
10-51697976-C-G		not specified	Uncertain significance (Jun 09, 2022)
10-51698022-C-G		not specified	Uncertain significance (Feb 09, 2023)
10-51698030-C-A		not specified	Uncertain significance (Nov 09, 2021)
10-51698076-G-A		not specified	Uncertain significance (Jun 17, 2022)
10-51698093-C-T		not specified	Uncertain significance (Jan 24, 2024)
10-51698157-G-C		not specified	Uncertain significance (Mar 30, 2022)
10-51698207-A-C		not specified	Uncertain significance (Feb 28, 2024)
10-51698228-C-G		not specified	Uncertain significance (Nov 30, 2021)
10-51698259-G-A		not specified	Uncertain significance (Nov 09, 2023)
10-51698300-G-A		not specified	Uncertain significance (Aug 23, 2021)
10-51698307-A-G		not specified	Uncertain significance (Dec 01, 2022)
10-51698313-T-C		not specified	Uncertain significance (May 23, 2023)
10-51698316-C-T		not specified	Likely benign (Feb 27, 2023)
10-51698427-G-A		not specified	Uncertain significance (Jan 31, 2024)
10-51698433-G-T		not specified	Uncertain significance (Jul 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CSTF2T	protein_coding	protein_coding	ENST00000331173	1	4109

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0864	0.912	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.904	298	345	0.863	0.0000174	3962
Missense in Polyphen		105	125.99	0.83339		1516
Synonymous	-0.416	126	120	1.05	0.00000595	1346
Loss of Function	2.74	5	17.3	0.289	9.47e-7	203

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a significant role in AAUAAA-independent mRNA polyadenylation in germ cells. Directly involved in the binding to pre-mRNAs (By similarity). {ECO:0000250}.
• Pathway: mRNA surveillance pathway - Homo sapiens (human);mRNA Processing;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)

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.420
• rvis_EVS: -0.62
• rvis_percentile_EVS: 17.16

Haploinsufficiency Scores

• pHI: 0.119
• hipred: N
• hipred_score: 0.427
• ghis: 0.560

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.989

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cstf2t
• Phenotype: reproductive system phenotype

Gene ontology

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