FUBP3

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

Basic information

Region (hg38): 9:130578965-130638352

Previous symbols: [ "FBP3" ]

Links

ENSG00000107164 ∙ NCBI:8939 ∙ OMIM:603536 ∙ HGNC:4005 ∙ Uniprot:Q96I24 ∙ 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 FUBP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FUBP3 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			33	1		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	1	0

Variants in FUBP3

This is a list of pathogenic ClinVar variants found in the FUBP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-130579741-G-A		not specified	Uncertain significance (Mar 19, 2024)
9-130595528-C-A		not specified	Uncertain significance (Mar 16, 2024)
9-130612458-C-T		not specified	Uncertain significance (Jul 26, 2022)
9-130612985-C-T		not specified	Uncertain significance (Mar 06, 2025)
9-130616396-G-A		not specified	Uncertain significance (Aug 19, 2021)
9-130616474-G-T		not specified	Uncertain significance (Feb 06, 2024)
9-130617800-C-T		not specified	Uncertain significance (Jul 16, 2024)
9-130617866-C-T		not specified	Uncertain significance (Sep 24, 2024)
9-130617879-A-G		not specified	Uncertain significance (Nov 20, 2024)
9-130617879-A-T		not specified	Uncertain significance (Jul 10, 2024)
9-130617887-A-C		not specified	Uncertain significance (Feb 05, 2024)
9-130620408-C-T		not specified	Uncertain significance (Feb 06, 2024)
9-130620417-C-T		not specified	Uncertain significance (Dec 21, 2022)
9-130620418-G-A		not specified	Uncertain significance (Oct 01, 2024)
9-130622786-G-T		not specified	Uncertain significance (Feb 27, 2023)
9-130622800-G-T		not specified	Uncertain significance (Dec 17, 2023)
9-130622807-C-T		not specified	Uncertain significance (Apr 09, 2024)
9-130623656-C-T		not specified	Uncertain significance (Jun 07, 2024)
9-130626373-G-A		not specified	Uncertain significance (May 25, 2022)
9-130626392-C-T		not specified	Likely benign (Oct 03, 2022)
9-130626404-G-C		not specified	Uncertain significance (Jan 30, 2024)
9-130626410-G-A		not specified	Uncertain significance (Aug 21, 2023)
9-130626421-G-T		not specified	Uncertain significance (Oct 31, 2023)
9-130626430-G-A		not specified	Uncertain significance (Oct 08, 2024)
9-130630693-C-T		not specified	Uncertain significance (Feb 20, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FUBP3	protein_coding	protein_coding	ENST00000319725	19	59388

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.798	0.202	124786	0	10	124796	0.0000401

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.17	222	334	0.665	0.0000195	3739
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.0000456	0.0000441
Middle Eastern	0.000111	0.000111
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.337
• hipred: Y
• hipred_score: 0.604
• ghis: 0.660

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.870

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fubp3

Gene ontology

• Biological process: transcription, DNA-templated;positive regulation of gene expression;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus;cytoplasm;membrane
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription activator activity, RNA polymerase II-specific;RNA binding;protein binding