USF3

upstream transcription factor family member 3

Basic information

Region (hg38): 3:113648385-113696646

Previous symbols: [ "KIAA2018" ]

Links

ENSG00000176542 ∙ NCBI:205717 ∙ OMIM:617568 ∙ HGNC:30494 ∙ Uniprot:Q68DE3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown
• Cowden disease (Supportive), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the USF3 gene.

• not_specified (241 variants)
• not_provided (12 variants)
• EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the USF3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001009899.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				3		3
missense			224	19	1	244
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	224	22	1

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
USF3	protein_coding	protein_coding	ENST00000316407	5	48262

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000101	124840	0	18	124858	0.0000721

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.793	1063	1.14e+3	0.934	0.0000563	14752
Missense in Polyphen		342	411.47	0.83117		5338
Synonymous	0.784	391	411	0.951	0.0000205	4573
Loss of Function	6.94	7	69.3	0.101	0.00000371	851

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000248	0.000247
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000555
Finnish	0.00	0.00
European (Non-Finnish)	0.000109	0.0000971
Middle Eastern	0.0000556	0.0000555
South Asian	0.0000752	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the negative regulation of epithelial- mesenchymal transition, the process by which epithelial cells lose their polarity and adhesion properties to become mesenchymal cells with enhanced migration and invasive properties. {ECO:0000269|PubMed:28011713}.

Intolerance Scores

• rvis_EVS: -0.71
• rvis_percentile_EVS: 14.5

Haploinsufficiency Scores

• pHI: 0.423
• hipred: Y
• hipred_score: 0.518
• ghis: 0.541

Mouse Genome Informatics

• Gene name: Usf3
• 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 by RNA polymerase II;negative regulation of epithelial to mesenchymal transition
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein dimerization activity