CSTF2T

protein-coding

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

Gene summary

Enables RNA binding activity. Predicted to be involved in mRNA 3'-end processing. Predicted to be located in nucleoplasm. Predicted to be part of mRNA cleavage and polyadenylation specificity factor complex. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_015235.3

Inheritance

—

ClinVar variants

U:88B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.29

Max pathogenic AF

—

Genomic locus

chr10:51,695,486-51,699,595

External References & Databases

Ensembl (ENSG00000177613)

Transcript & Mutation Effects

hg38 • Region Span ~4.1 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 CSTF2T variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 89

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015235.3. 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				2 clinvar		2
missense			88 clinvar	3 clinvar	1 clinvar	92
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	88	5	1	94

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015235.3	RefSeq	NP_056050.1	1	MANE Select
ENST00000331173.6	Ensembl	ENSP00000332444.4	1	MANE Select

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)
RNA Polymerase II Transcription
Metabolism of RNA

Biological Process

mRNA splicing, via spliceosome
termination of RNA polymerase II transcription
mRNA 3'-end processing
pre-mRNA cleavage required for polyadenylation

Molecular Function

RNA binding
mRNA binding
protein binding

Cellular Component

nucleoplasm
mRNA cleavage and polyadenylation specificity factor complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000331173
Coding exons: 1
Length: 4109
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.904	298	345	0.863	0.0000174	3962
Missense (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

Population LoF Frequency

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

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.101

Intolerance Scores

LoFtool: 0.420
RVIS EVS: -0.62
RVIS percentile EVS: 17.16

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.989

Gene Damage Prediction

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