FUBP3

protein-coding

far upstream element binding protein 3, the group of MicroRNA protein coding host genes

Gene summary

Enables single-stranded DNA binding activity. Involved in DNA-templated transcription; positive regulation of DNA-templated transcription; and positive regulation of gene expression. Acts upstream of or within positive regulation of transcription by RNA polymerase II. Located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

FBP3

MANE transcript

NM_003934.2

Inheritance

—

ClinVar variants

U:73B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.19

Max pathogenic AF

—

Genomic locus

chr9:130,578,965-130,638,352

External References & Databases

Ensembl (ENSG00000107164)

Transcript & Mutation Effects

hg38 • Region Span ~59.4 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 FUBP3 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 68

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003934.2. 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			1 clinvar			1
missense			70 clinvar	4 clinvar		74
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	73	4	0	77

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 58 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003934.2	RefSeq	NP_003925.1	19	MANE Select
ENST00000319725.10	Ensembl	ENSP00000318177.9	19	MANE Select
ENST00000650723.1	Ensembl	ENSP00000499109.1	2	Standard
ENST00000699747.1	Ensembl	ENSP00000514557.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

transcription, DNA-templated
positive regulation of gene expression
positive regulation of transcription, DNA-templated
positive regulation of transcription by RNA polymerase II

Molecular Function

RNA polymerase II proximal promoter sequence-specific DNA binding
DNA-binding transcription activator activity, RNA polymerase II-specific
RNA binding
protein binding

Cellular Component

nucleus
cytoplasm
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000319725
Coding exons: 19
Length: 59388
Individuals with no LoFs: 124786
Homozygous LoFs: 0
Heterozygous LoFs: 10
Defined: 124796
p: 0.0000401

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.17	222	334	0.665	0.0000195	3739
Missense (PolyPhen)		37	97.096	0.38107		1060
Synonymous	0.879	115	128	0.901	0.00000860	1103
Loss of Function	4.49	7	36.1	0.194	0.00000183	396

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000065	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000046	0.000044	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May interact with single-stranded DNA from the far- upstream element (FUSE). May activate gene expression.;

Recessive Scores

pRec: 0.108

Intolerance Scores

LoFtool: 0.423
RVIS EVS: -0.51
RVIS percentile EVS: 21.56

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.870

Gene Damage Prediction

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