UBP1

upstream binding protein 1

Basic information

Region (hg38): 3:33388335-33441371

Links

ENSG00000153560 ∙ NCBI:7342 ∙ OMIM:609784 ∙ HGNC:12507 ∙ Uniprot:Q9NZI7 ∙ 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 UBP1 gene.

• Inborn genetic diseases (15 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBP1 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			12	3		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	3	0

Variants in UBP1

This is a list of pathogenic ClinVar variants found in the UBP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-33393346-C-A		not specified	Uncertain significance (Dec 16, 2022)
3-33396189-T-C		not specified	Likely benign (Jul 14, 2021)
3-33396229-G-C		not specified	Uncertain significance (Sep 17, 2021)
3-33396246-G-A		not specified	Uncertain significance (Oct 03, 2022)
3-33400264-T-C		not specified	Uncertain significance (May 23, 2023)
3-33400967-C-T		not specified	Likely benign (May 08, 2023)
3-33400996-T-C		not specified	Uncertain significance (Dec 09, 2023)
3-33402834-G-A		not specified	Uncertain significance (Jan 29, 2024)
3-33402835-A-G		not specified	Uncertain significance (Jan 29, 2024)
3-33402853-G-T		not specified	Likely benign (Nov 10, 2022)
3-33409247-T-C		not specified	Uncertain significance (Mar 16, 2022)
3-33409459-T-C		not specified	Uncertain significance (Mar 29, 2022)
3-33411657-G-C		not specified	Uncertain significance (Apr 19, 2023)
3-33411684-A-G		not specified	Uncertain significance (Feb 01, 2023)
3-33416804-T-A		not specified	Uncertain significance (Nov 08, 2022)
3-33425667-G-C		not specified	Uncertain significance (Apr 25, 2023)
3-33439782-G-A		not specified	Uncertain significance (Sep 07, 2022)
3-33439812-A-C		not specified	Uncertain significance (Jul 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UBP1	protein_coding	protein_coding	ENST00000283629	16	53036

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000581	125739	0	5	125744	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.98	155	301	0.516	0.0000159	3554
Missense in Polyphen		23	81.892	0.28086		1005
Synonymous	0.880	99	111	0.894	0.00000616	1001
Loss of Function	5.39	0	33.8	0.00	0.00000167	394

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000356	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000329	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as a transcriptional activator in a promoter context-dependent manner. Modulates the placental expression of CYP11A1. Involved in regulation of the alpha-globin gene in erythroid cells. Activation of the alpha-globin promoter in erythroid cells is via synergistic interaction with TFCP2 (By similarity). Involved in regulation of the alpha-globin gene in erythroid cells. Binds strongly to sequences around the HIV-1 initiation site and weakly over the TATA-box. Represses HIV-1 transcription by inhibiting the binding of TFIID to the TATA-box. {ECO:0000250, ECO:0000269|PubMed:10644752, ECO:0000269|PubMed:2006421, ECO:0000269|PubMed:8114710}.

Recessive Scores

• pRec: 0.131

Intolerance Scores

• loftool: 0.100
• rvis_EVS: -0.23
• rvis_percentile_EVS: 37.32

Haploinsufficiency Scores

• pHI: 0.792
• hipred: Y
• hipred_score: 0.728
• ghis: 0.598

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.116

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ubp1
• Phenotype: muscle 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); 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); growth/size/body region phenotype; embryo phenotype

Gene ontology

• Biological process: angiogenesis;regulation of transcription by RNA polymerase II;viral genome replication;negative regulation of transcription, DNA-templated
• Cellular component: nucleus;nucleoplasm;cytosol
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;transcription corepressor activity;sequence-specific DNA binding