GTF2I

general transcription factor IIi, the group of General transcription factors

Basic information

Region (hg38): 7:74650231-74760692

Previous symbols: [ "WBSCR6" ]

Links

ENSG00000263001 ∙ NCBI:2969 ∙ OMIM:601679 ∙ HGNC:4659 ∙ Uniprot:P78347 ∙ 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 GTF2I gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GTF2I 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			11	1		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)				1		1
splice region						0
non coding						0
Total	0	0	11	4	0

Variants in GTF2I

This is a list of pathogenic ClinVar variants found in the GTF2I region.

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

Position	Type	Phenotype	Significance	ClinVar
7-74689159-G-A		not specified	Uncertain significance (Apr 30, 2024)
7-74689178-C-T		not specified	Uncertain significance (Oct 12, 2024)
7-74691092-A-G			Likely benign (Aug 01, 2024)
7-74698963-G-C		not specified	Uncertain significance (Sep 03, 2024)
7-74699012-C-T		not specified	Uncertain significance (Apr 08, 2024)
7-74699078-A-G			Uncertain significance (Apr 06, 2017)
7-74700273-G-A		not specified	Uncertain significance (Mar 29, 2023)
7-74700309-T-C		not specified	Uncertain significance (Nov 28, 2024)
7-74700415-C-T		not specified	Uncertain significance (Mar 15, 2024)
7-74705166-G-T		not specified	Uncertain significance (Dec 07, 2021)
7-74705182-C-T		not specified	Uncertain significance (Oct 04, 2024)
7-74705211-G-A		not specified	Uncertain significance (Jan 08, 2024)
7-74711035-T-G		not specified	Uncertain significance (Nov 11, 2024)
7-74714904-A-C		not specified	Uncertain significance (Oct 04, 2024)
7-74733979-G-C		not specified	Uncertain significance (Feb 17, 2023)
7-74738082-C-G			Likely benign (Aug 01, 2023)
7-74738092-C-T		not specified	Uncertain significance (Jan 04, 2024)
7-74743485-G-A			Benign (Nov 01, 2024)
7-74744778-G-A		not specified	Uncertain significance (Aug 20, 2024)
7-74744818-C-T		not specified	Uncertain significance (Jan 11, 2023)
7-74744887-C-T		not specified	Uncertain significance (Apr 25, 2023)
7-74744931-G-A		not specified	Uncertain significance (Nov 07, 2022)
7-74748058-G-T			Likely benign (Nov 01, 2023)
7-74752088-A-G			Likely benign (Dec 01, 2022)
7-74753169-G-A		not specified	Uncertain significance (Dec 19, 2022)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Interacts with the basal transcription machinery by coordinating the formation of a multiprotein complex at the C-FOS promoter, and linking specific signal responsive activator complexes. Promotes the formation of stable high-order complexes of SRF and PHOX1 and interacts cooperatively with PHOX1 to promote serum-inducible transcription of a reporter gene deriven by the C- FOS serum response element (SRE). Acts as a coregulator for USF1 by binding independently two promoter elements, a pyrimidine-rich initiator (Inr) and an upstream E-box. Required for the formation of functional ARID3A DNA-binding complexes and for activation of immunoglobulin heavy-chain transcription upon B-lymphocyte activation. {ECO:0000269|PubMed:10373551, ECO:0000269|PubMed:11373296, ECO:0000269|PubMed:16738337}.
• Disease: DISEASE: Note=GTF2I is located in the Williams-Beuren syndrome (WBS) critical region. WBS results from a hemizygous deletion of several genes on chromosome 7q11.23, thought to arise as a consequence of unequal crossing over between highly homologous low-copy repeat sequences flanking the deleted region. Haploinsufficiency of GTF2I may be the cause of certain cardiovascular and musculo-skeletal abnormalities observed in the disease.
• Pathway: Basal transcription factors - Homo sapiens (human);cGMP-PKG signaling pathway - Homo sapiens (human);Herpes simplex infection - Homo sapiens (human);B Cell Receptor Signaling Pathway;BCR;TNFalpha (Consensus)

Recessive Scores

• pRec: 0.436

Haploinsufficiency Scores

• pHI: 0.447
• hipred: Y
• hipred_score: 0.740
• ghis: 0.399

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.993

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gtf2i
• Phenotype: craniofacial phenotype; cellular phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system 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); reproductive system 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); embryo phenotype

Gene ontology

• Biological process: regulation of transcription, DNA-templated;transcription by RNA polymerase II;transcription initiation from RNA polymerase II promoter;signal transduction;negative regulation of angiogenesis;negative regulation of cytosolic calcium ion concentration
• Cellular component: nucleus;nucleoplasm;cytoplasm;membrane
• Molecular function: DNA binding;DNA-binding transcription factor activity;protein binding