USF2

protein-coding

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

Gene summary

This gene encodes a member of the basic helix-loop-helix leucine zipper family of transcription factors. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs and is involved in regulating multiple cellular processes. [provided by RefSeq, Mar 2016]

MANE transcript

NM_003367.4

Inheritance

—

ClinVar variants

U:56

Top phenotype

Prostate cancer

gnomAD constraint

pLI —, LoF o/e 0.05

Max pathogenic AF

—

Genomic locus

chr19:35,268,962-35,279,821

External References & Databases

Ensembl (ENSG00000105698)

Transcript & Mutation Effects

hg38 • Region Span ~10.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to USF2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 46

Prostate cancerTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003367.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			49 clinvar			49
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	56	0	0	56

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 22 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003367.4	RefSeq	NP_003358.1	10	MANE Select
ENST00000222305.8	Ensembl	ENSP00000222305.2	10	MANE Select
NM_001321150.2	RefSeq	NP_001308079.1	8	Standard
NM_207291.3	RefSeq	NP_997174.1	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Signal Transduction
Signaling by Nuclear Receptors
Estrogen-dependent gene expression
ESR-mediated signaling
Validated transcriptional targets of AP1 family members Fra1 and Fra2

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

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

Cellular Component

nucleus
nucleoplasm
intracellular membrane-bounded organelle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000222305
Coding exons: 10
Length: 10844
Individuals with no LoFs: 125690
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 125691
p: 0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.89	106	177	0.599	0.0000110	2202
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec: 0.333

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 1.00

Gene Damage Prediction

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