USF1

upstream transcription factor 1, the group of Basic helix-loop-helix proteins

Basic information

Region (hg38): 1:161039250-161045977

Links

ENSG00000158773 ∙ NCBI:7391 ∙ OMIM:191523 ∙ HGNC:12593 ∙ Uniprot:P22415 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hyperlipidemia, combined, 1 (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the USF1 gene.

• Inborn genetic diseases (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the USF1 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			3			3
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	3	0	0

Variants in USF1

This is a list of pathogenic ClinVar variants found in the USF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-161039733-G-A		Hyperlipidemia, familial combined, susceptibility to	risk factor (Sep 01, 2005)
1-161039928-T-C		not specified	Uncertain significance (Nov 21, 2022)
1-161040209-C-A		not specified	Uncertain significance (Dec 30, 2023)
1-161040229-C-G		not specified	Uncertain significance (Mar 06, 2023)
1-161040251-A-G		not specified	Uncertain significance (Jun 03, 2022)
1-161040573-G-A		not specified	Uncertain significance (Jul 26, 2023)
1-161040972-C-T		Hyperlipidemia, familial combined, susceptibility to	risk factor (Sep 01, 2005)
1-161041352-T-C		not specified	Uncertain significance (Jan 09, 2024)
1-161041845-G-A		not specified	Uncertain significance (Jan 19, 2024)
1-161042154-C-T		not specified	Uncertain significance (Nov 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
USF1	protein_coding	protein_coding	ENST00000368021	10	6727

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0235	0.976	125325	0	423	125748	0.00168

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.14	107	190	0.563	0.0000113	2006
Missense in Polyphen		27	63.998	0.42189		692
Synonymous	0.107	70	71.2	0.984	0.00000411	620
Loss of Function	3.02	7	22.5	0.312	0.00000136	208

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00732	0.00699
Ashkenazi Jewish	0.000701	0.000695
East Asian	0.000771	0.000761
Finnish	0.00291	0.00287
European (Non-Finnish)	0.00182	0.00179
Middle Eastern	0.000771	0.000761
South Asian	0.0000656	0.0000653
Other	0.00282	0.00277

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor that binds to a symmetrical DNA sequence (E-boxes) (5'-CACGTG-3') that is found in a variety of viral and cellular promoters.
• Disease: DISEASE: Hyperlipidemia combined 1 (HYPLIP1) [MIM:602491]: A disorder characterized by a variable pattern of elevated levels of serum total cholesterol, triglycerides or both. It is observed in a percentage of individuals with premature coronary heart disease. {ECO:0000269|PubMed:14991056}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.
• Pathway: Signal Transduction;Signaling by Nuclear Receptors;Estrogen-dependent gene expression;ESR-mediated signaling;Signaling mediated by p38-alpha and p38-beta (Consensus)

Recessive Scores

• pRec: 0.637

Intolerance Scores

• loftool: 0.273
• rvis_EVS: -0.41
• rvis_percentile_EVS: 26.23

Haploinsufficiency Scores

• pHI: 0.298
• hipred: Y
• hipred_score: 0.735
• ghis: 0.630

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Usf1
• 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); normal 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)

Gene ontology

• Biological process: regulation of transcription from RNA polymerase II promoter by glucose;positive regulation of transcription from RNA polymerase II promoter by glucose;response to hypoxia;glucose metabolic process;regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;response to UV;late viral transcription;cellular response to insulin stimulus;glucose homeostasis;positive regulation of transcription by RNA polymerase II;carbon catabolite regulation of transcription;negative regulation of fibrinolysis;lipid homeostasis
• Cellular component: nuclear chromatin;nucleus;nucleoplasm;transcription factor complex;NURF complex;Set1C/COMPASS complex
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;double-stranded DNA binding;protein binding;enzyme binding;protein kinase binding;identical protein binding;protein homodimerization activity;histone deacetylase binding;bHLH transcription factor binding;sequence-specific DNA binding;protein heterodimerization activity