FUBP1

far upstream element binding protein 1

Basic information

Region (hg38): 1:77944055-77979110

Previous symbols: [ "FUBP" ]

Links

ENSG00000162613 ∙ NCBI:8880 ∙ OMIM:603444 ∙ HGNC:4004 ∙ Uniprot:Q96AE4 ∙ 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 FUBP1 gene.

• not_specified (52 variants)
• not_provided (3 variants)
• Breast_ductal_adenocarcinoma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FUBP1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003902.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			2		2	4
missense			56			56
nonsense			2			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			10			10
Total	0	0	70	0	2

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FUBP1	protein_coding	protein_coding	ENST00000370768	20	35055

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		124662	0	4	124666	0.0000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.97	203	362	0.561	0.0000179	4126
Missense in Polyphen		52	135.28	0.38438		1568
Synonymous	-0.174	116	114	1.02	0.00000572	1288
Loss of Function	5.80	1	41.1	0.0243	0.00000196	483

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000381	0.0000381
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000289	0.0000265
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. May act both as activator and repressor of transcription. {ECO:0000269|PubMed:8125259}.

Recessive Scores

• pRec: 0.170

Intolerance Scores

• rvis_EVS: -0.29
• rvis_percentile_EVS: 33.2

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.988

Gene Damage Prediction

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

Gene ontology

• Biological process: regulation of transcription, DNA-templated;transcription by RNA polymerase II;positive regulation of gene expression
• Cellular component: nucleus;nucleoplasm
• Molecular function: single-stranded DNA binding;DNA-binding transcription factor activity;RNA binding;protein binding