CSTF2

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

Basic information

Region (hg38): X:100820391-100841520

Links

ENSG00000101811 ∙ NCBI:1478 ∙ OMIM:300907 ∙ HGNC:2484 ∙ Uniprot:P33240 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder, X-linked 113	XL	General	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	Neurologic	32816001

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CSTF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CSTF2 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	1	2
missense			17	1		18
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	17	3	2

Variants in CSTF2

This is a list of pathogenic ClinVar variants found in the CSTF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-100820441-C-T		not specified	Uncertain significance (May 22, 2023)
X-100822260-C-T			Likely benign (Jun 08, 2018)
X-100822262-A-C		Intellectual developmental disorder, X-linked 113	Pathogenic (Feb 06, 2024)
X-100823307-C-T		not specified	Uncertain significance (Oct 09, 2024)
X-100823876-A-G			Benign (Apr 26, 2018)
X-100824150-A-G		not specified	Uncertain significance (Jan 24, 2025)
X-100824151-C-T		not specified	Uncertain significance (Aug 02, 2021)
X-100824169-C-T		not specified	Uncertain significance (Aug 02, 2022)
X-100824216-A-G		not specified	Uncertain significance (Dec 31, 2024)
X-100824251-G-C		not specified	Uncertain significance (Jan 04, 2022)
X-100826656-C-T		not specified	Uncertain significance (Jan 14, 2025)
X-100826679-A-G		not specified	Uncertain significance (Oct 23, 2024)
X-100826718-G-A		not specified	Uncertain significance (Jan 03, 2024)
X-100831614-G-A		not specified	Uncertain significance (May 09, 2023)
X-100832774-C-T		not specified	Uncertain significance (May 23, 2023)
X-100832804-C-T		not specified	Uncertain significance (Oct 01, 2024)
X-100832842-C-T			Benign (Dec 31, 2019)
X-100832853-T-A		not specified	Uncertain significance (Feb 13, 2025)
X-100833191-C-T		not specified	Uncertain significance (Aug 09, 2021)
X-100833252-C-T		not specified	Uncertain significance (Jan 12, 2024)
X-100833269-C-T		not specified	Uncertain significance (Dec 13, 2024)
X-100833270-G-A		not specified	Uncertain significance (Mar 07, 2025)
X-100833284-C-T		not specified	Uncertain significance (Jan 26, 2022)
X-100833300-G-A		not specified	Uncertain significance (Mar 01, 2023)
X-100833304-AATGGAGGCCCGAGCG-A			Likely benign (Dec 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CSTF2	protein_coding	protein_coding	ENST00000372972	13	20538

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000405	116298	1	0	116299	0.00000430

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.43	88	236	0.372	0.0000181	3723
Missense in Polyphen		28	107.95	0.25938		1740
Synonymous	1.09	67	79.3	0.845	0.00000599	1191
Loss of Function	4.39	0	22.4	0.00	0.00000190	339

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)	0.0000131	0.00000969
Middle Eastern	0.00	0.00
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. This subunit is directly involved in the binding to pre-mRNAs (By similarity). {ECO:0000250, ECO:0000269|PubMed:9199325}.
• Pathway: mRNA surveillance pathway - Homo sapiens (human);mRNA Processing;tRNA 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;tRNA processing in the nucleus;mRNA Splicing;mRNA 3,-end processing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.497
• rvis_EVS: 0.24
• rvis_percentile_EVS: 68.98

Haploinsufficiency Scores

• pHI: 0.274
• hipred: Y
• hipred_score: 0.684
• ghis: 0.541

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.973

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cstf2
• Phenotype: embryo phenotype

Gene ontology

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