FUBP1

far upstream element binding protein 1

Basic information

Region (hg38): 1:77944054-77979110

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.

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.

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					2	2
missense			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	17	0	2

Variants in FUBP1

This is a list of pathogenic ClinVar variants found in the FUBP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-77949279-G-A		not specified	Uncertain significance (Apr 14, 2023)
1-77949280-T-C		not specified	not provided (Sep 19, 2013)
1-77956607-G-A		not specified	Uncertain significance (Feb 09, 2023)
1-77956653-C-T		not specified	Uncertain significance (Jun 29, 2023)
1-77956666-C-T		Breast ductal adenocarcinoma	Uncertain significance (Jul 20, 2015)
1-77956689-T-C		not specified	not provided (Sep 19, 2013)
1-77960243-G-A		not specified	Uncertain significance (Oct 02, 2023)
1-77960359-G-C		not specified	Uncertain significance (Sep 27, 2021)
1-77960411-G-A		not specified	Uncertain significance (Oct 03, 2023)
1-77960491-G-A		not specified	Uncertain significance (Nov 03, 2022)
1-77962787-T-C		not specified	Uncertain significance (Aug 12, 2021)
1-77962829-T-A		not specified	Uncertain significance (Mar 12, 2024)
1-77962829-T-C		not specified	Uncertain significance (Oct 03, 2022)
1-77962911-G-A			Benign (Aug 08, 2017)
1-77963621-A-G		not specified	Uncertain significance (Jun 07, 2024)
1-77963630-A-G		not specified	Uncertain significance (Feb 23, 2023)
1-77963642-G-T		not specified	Uncertain significance (Dec 06, 2023)
1-77963723-G-C		not specified	Benign (Mar 28, 2016)
1-77964111-C-T		not specified	not provided (Sep 19, 2013)
1-77964964-C-T		not specified	Uncertain significance (Jan 16, 2024)
1-77965157-G-A		not specified	Uncertain significance (Oct 04, 2022)
1-77965167-C-A		not specified	not provided (Sep 19, 2013)
1-77965207-C-A		not specified	Uncertain significance (Dec 18, 2023)
1-77966724-C-T		not specified	Uncertain significance (Nov 17, 2023)
1-77968172-T-G		not specified	not provided (Sep 19, 2013)

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
1.00	0.00000197	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

Haploinsufficiency Scores

• pHI: 0.609
• hipred: Y
• hipred_score: 0.783
• ghis: 0.608

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

Mouse Genome Informatics

• Gene name: Fubp1
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype; respiratory system phenotype; liver/biliary system phenotype; immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype

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