GTF2IRD1

GTF2I repeat domain containing 1

Basic information

Region (hg38): 7:74453789-74602605

Previous symbols: [ "WBSCR11" ]

Links

ENSG00000006704 ∙ NCBI:9569 ∙ OMIM:604318 ∙ HGNC:4661 ∙ Uniprot:Q9UHL9 ∙ 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 GTF2IRD1 gene.

• not provided (52 variants)
• Inborn genetic diseases (41 variants)
• not specified (2 variants)
• GTF2IRD1-related condition (1 variants)
• Childhood-onset schizophrenia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GTF2IRD1 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				29	11	40
missense		1	40	5	1	47
nonsense			3			3
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding				3	2	5
Total	0	1	43	37	14

Variants in GTF2IRD1

This is a list of pathogenic ClinVar variants found in the GTF2IRD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-74508107-C-T			Likely benign (Oct 17, 2018)
7-74508112-C-T		not specified	Uncertain significance (Aug 08, 2023)
7-74508119-C-T			Likely benign (Mar 01, 2023)
7-74508149-G-A		GTF2IRD1-related disorder	Likely benign (Dec 31, 2019)
7-74508157-G-A		not specified	Uncertain significance (Jul 13, 2022)
7-74512837-C-T		not specified	Uncertain significance (Jun 07, 2022)
7-74512853-C-T		GTF2IRD1-related disorder	Likely benign (Sep 05, 2019)
7-74512889-C-A		not specified	Uncertain significance (Jul 20, 2021)
7-74512890-G-A		not specified	Uncertain significance (Aug 22, 2023)
7-74512899-G-T		not specified	Uncertain significance (May 17, 2023)
7-74515362-A-G		not specified	Uncertain significance (Nov 09, 2023)
7-74515390-G-A		not specified	Uncertain significance (Oct 20, 2023)
7-74515402-G-C		not specified	Uncertain significance (Dec 13, 2021)
7-74515421-G-A		GTF2IRD1-related disorder	Benign/Likely benign (Feb 01, 2024)
7-74515421-G-C		GTF2IRD1-related disorder	Likely benign (Mar 18, 2019)
7-74515509-C-T			Likely benign (Nov 01, 2021)
7-74515510-G-A		not specified	Uncertain significance (Mar 14, 2023)
7-74515522-G-A		not specified	Uncertain significance (Jun 01, 2023)
7-74518158-C-G		GTF2IRD1-related disorder	Benign/Likely benign (Jun 01, 2023)
7-74518164-G-T			Benign (May 01, 2023)
7-74518167-G-A			Benign (Dec 31, 2019)
7-74518191-C-T		GTF2IRD1-related disorder	Likely benign (Dec 31, 2019)
7-74518227-C-T			Likely benign (Jun 28, 2018)
7-74518230-A-G		GTF2IRD1-related disorder	Benign (Oct 17, 2019)
7-74518273-C-T		not specified	Uncertain significance (Aug 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GTF2IRD1	protein_coding	protein_coding	ENST00000455841	26	148812

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.900	0.0996	125731	0	16	125747	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.66	444	632	0.702	0.0000421	6309
Missense in Polyphen		114	200.23	0.56934		2020
Synonymous	0.327	269	276	0.975	0.0000201	2004
Loss of Function	5.36	10	51.5	0.194	0.00000282	578

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000294	0.0000294
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000233	0.000231
European (Non-Finnish)	0.0000531	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be a transcription regulator involved in cell-cycle progression and skeletal muscle differentiation. May repress GTF2I transcriptional functions, by preventing its nuclear residency, or by inhibiting its transcriptional activation. May contribute to slow-twitch fiber type specificity during myogenesis and in regenerating muscles. Binds troponin I slow-muscle fiber enhancer (USE B1). Binds specifically and with high affinity to the EFG sequences derived from the early enhancer of HOXC8 (By similarity). {ECO:0000250, ECO:0000269|PubMed:11438732}.
• Disease: DISEASE: Note=GTF2IRD1 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 GTF2IRD1 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) (Consensus)

Recessive Scores

• pRec: 0.160

Intolerance Scores

• loftool: 0.305
• rvis_EVS: -1.39
• rvis_percentile_EVS: 4.31

Haploinsufficiency Scores

• pHI: 0.342
• hipred: Y
• hipred_score: 0.759
• ghis: 0.511

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.733

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gtf2ird1
• Phenotype: craniofacial phenotype; muscle phenotype; cellular phenotype; homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); 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); 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); 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); growth/size/body region 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); skeleton phenotype; respiratory system phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; neoplasm; pigmentation phenotype

Gene ontology

• Biological process: regulation of transcription, DNA-templated;regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;multicellular organism development;transition between slow and fast fiber
• Cellular component: nucleus;nucleoplasm;cytosol
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;protein binding