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.

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.

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				2		2
missense			94	8		102
nonsense						0
start loss						0
frameshift						0
inframe indel				1	1	2
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	94	11	2

Variants in USF3

This is a list of pathogenic ClinVar variants found in the USF3 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-113651163-G-T			Benign (Jul 15, 2020)
3-113655042-C-T		not specified	Uncertain significance (Apr 09, 2024)
3-113655044-A-G		not specified	Uncertain significance (Sep 27, 2021)
3-113655157-C-A		not specified	Uncertain significance (Dec 19, 2022)
3-113655282-T-C		not specified	Uncertain significance (Apr 18, 2023)
3-113655292-A-C		not specified	Uncertain significance (Dec 28, 2022)
3-113655324-T-C		not specified	Uncertain significance (Sep 06, 2022)
3-113655356-G-A		not specified	Uncertain significance (Feb 03, 2022)
3-113655503-G-A		not specified	Uncertain significance (Jan 05, 2022)
3-113655527-G-A		not specified	Uncertain significance (Aug 30, 2021)
3-113655562-G-T		not specified	Uncertain significance (May 09, 2022)
3-113655566-C-G		not specified	Uncertain significance (Feb 27, 2024)
3-113655581-C-T		not specified	Uncertain significance (Dec 03, 2021)
3-113655584-T-C		not specified	Uncertain significance (Nov 06, 2023)
3-113655606-G-A		not specified	Uncertain significance (Apr 08, 2023)
3-113655612-G-A		not specified	Uncertain significance (Aug 15, 2024)
3-113655632-G-C		not specified	Uncertain significance (Aug 15, 2024)
3-113655636-G-A		not specified	Uncertain significance (Apr 20, 2024)
3-113655638-G-A		not specified	Uncertain significance (Sep 14, 2022)
3-113655710-C-T		not specified	Uncertain significance (Feb 27, 2023)
3-113655732-C-G		not specified	Uncertain significance (Jun 10, 2024)
3-113655770-T-C		not specified	Uncertain significance (Sep 03, 2024)
3-113655780-G-A		not specified	Conflicting classifications of pathogenicity (Dec 01, 2022)
3-113655920-T-C		not specified	Uncertain significance (Dec 05, 2022)
3-113655941-T-C		not specified	Uncertain significance (Oct 24, 2024)

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