CSTF1

protein-coding

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

Gene summary

This gene encodes one of three subunits which combine to form cleavage stimulation factor (CSTF). CSTF is involved in the polyadenylation and 3'end cleavage of pre-mRNAs. Similar to mammalian G protein beta subunits, this protein contains transducin-like repeats. Several transcript variants with different 5' UTR, but encoding the same protein, have been found for this gene. [provided by RefSeq, Jul 2008]

MANE transcript

NM_001324.3

Inheritance

—

ClinVar variants

U:34

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.11

Max pathogenic AF

—

Genomic locus

chr20:56,392,371-56,406,362

External References & Databases

Ensembl (ENSG00000101138)

Transcript & Mutation Effects

hg38 • Region Span ~14.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CSTF1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 26

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001324.3. 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.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			30 clinvar			30
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	34	0	0	34

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 35 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001324.3	RefSeq	NP_001315.1	5	MANE Select
ENST00000217109.9	Ensembl	ENSP00000217109.4	5	MANE Select
NM_001033521.2	RefSeq	NP_001028693.1	5	Standard
NM_001033522.2	RefSeq	NP_001028694.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

mRNA surveillance pathway - Homo sapiens (human)
mRNA Processing
Gene expression (Transcription)
polyadenylation of mrna
RNA Polymerase II Transcription

Biological Process

mRNA splicing, via spliceosome
termination of RNA polymerase II transcription
mRNA 3'-end processing

Molecular Function

RNA binding
protein binding

Cellular Component

nucleoplasm
mRNA cleavage stimulating factor complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000217109
Coding exons: 5
Length: 12092
Individuals with no LoFs: 125741
Homozygous LoFs: 0
Heterozygous LoFs: 3
Defined: 125744
p: 0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.41	110	267	0.413	0.0000161	2830
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000055	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000088	0.0000088	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec: 0.113

Intolerance Scores

LoFtool: 0.171
RVIS EVS: -0.71
RVIS percentile EVS: 14.4

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.996

Gene Damage Prediction

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