USF2

upstream transcription factor 2, c-fos interacting, the group of Basic helix-loop-helix proteins

Basic information

Region (hg38): 19:35268962-35279821

Links

ENSG00000105698 ∙ NCBI:7392 ∙ OMIM:600390 ∙ HGNC:12594 ∙ Uniprot:Q15853 ∙ 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 USF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the USF2 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			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	0

Variants in USF2

This is a list of pathogenic ClinVar variants found in the USF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-35269114-G-C		not specified	Uncertain significance (Oct 20, 2023)
19-35269139-C-T		not specified	Uncertain significance (Apr 18, 2023)
19-35269447-C-A		not specified	Uncertain significance (Dec 28, 2023)
19-35269466-C-T		not specified	Uncertain significance (Nov 27, 2024)
19-35269470-G-T		not specified	Uncertain significance (Dec 22, 2023)
19-35269617-T-G		not specified	Uncertain significance (Apr 24, 2024)
19-35269623-T-G		not specified	Uncertain significance (May 15, 2023)
19-35269656-A-G		not specified	Uncertain significance (Jun 24, 2022)
19-35269656-A-T		not specified	Uncertain significance (Jun 18, 2024)
19-35269676-C-T		not specified	Uncertain significance (Jan 23, 2024)
19-35269695-G-A		not specified	Uncertain significance (Jun 28, 2024)
19-35269845-G-A		not specified	Uncertain significance (Jun 16, 2023)
19-35269845-G-C		not specified	Uncertain significance (Oct 10, 2023)
19-35269887-G-A		not specified	Uncertain significance (Oct 29, 2024)
19-35269912-C-G		not specified	Uncertain significance (Oct 12, 2024)
19-35269923-G-C		not specified	Uncertain significance (Mar 20, 2024)
19-35269948-G-A		not specified	Uncertain significance (Oct 27, 2022)
19-35269977-C-T		not specified	Uncertain significance (Aug 30, 2021)
19-35270495-G-A		not specified	Uncertain significance (Dec 09, 2023)
19-35270510-G-A		not specified	Uncertain significance (Aug 16, 2021)
19-35270510-G-T		not specified	Uncertain significance (Jan 02, 2024)
19-35270514-G-A		Malignant tumor of prostate	Uncertain significance (-)
19-35270550-C-A		not specified	Uncertain significance (May 26, 2024)
19-35270552-A-G		not specified	Uncertain significance (Aug 11, 2022)
19-35270769-A-C		not specified	Uncertain significance (Mar 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
USF2	protein_coding	protein_coding	ENST00000222305	10	10844

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.993	0.00747	125690	0	1	125691	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.89	106	177	0.599	0.0000110	2202
Missense in Polyphen		34	70.555	0.48189		746
Synonymous	-0.148	72	70.4	1.02	0.00000486	668
Loss of Function	3.83	1	19.0	0.0525	0.00000115	203

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	0.0000462	0.0000462
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

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.
• Pathway: Signal Transduction;Signaling by Nuclear Receptors;Estrogen-dependent gene expression;ESR-mediated signaling;Validated transcriptional targets of AP1 family members Fra1 and Fra2 (Consensus)

Recessive Scores

• pRec: 0.333

Haploinsufficiency Scores

• pHI: 0.265
• hipred: Y
• hipred_score: 0.642
• ghis: 0.577

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• 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: Usf2
• Phenotype: 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); reproductive system phenotype; pigmentation phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); limbs/digits/tail 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); 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); growth/size/body region phenotype

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;transcription by RNA polymerase II;lactation;late viral transcription;positive regulation of transcription by RNA polymerase II;lipid homeostasis
• Cellular component: nucleus;nucleoplasm;intracellular membrane-bounded organelle
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;protein binding;protein homodimerization activity;bHLH transcription factor binding;sequence-specific DNA binding;protein heterodimerization activity