GTF2IRD2

GTF2I repeat domain containing 2

Basic information

Region (hg38): 7:74796151-74851605

Links

ENSG00000196275 ∙ NCBI:84163 ∙ OMIM:608899 ∙ HGNC:30775 ∙ Uniprot:Q86UP8 ∙ 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 GTF2IRD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GTF2IRD2 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	1	3
missense			12	2	1	15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	4	2

Variants in GTF2IRD2

This is a list of pathogenic ClinVar variants found in the GTF2IRD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-74797366-G-A			Benign (Dec 01, 2024)
7-74797820-G-A			Likely benign (Feb 01, 2025)
7-74819594-G-A			Likely benign (Jul 01, 2022)
7-74819984-A-G		not specified	Uncertain significance (Jul 12, 2023)
7-74819990-G-T		not specified	Uncertain significance (Jan 18, 2022)
7-74822435-C-T		not specified	Uncertain significance (Apr 26, 2023)
7-74822675-G-A			Likely benign (Nov 01, 2024)
7-74822678-G-A		not specified	Uncertain significance (Feb 16, 2023)
7-74822679-C-A		not specified	Uncertain significance (Feb 16, 2023)
7-74822732-A-G		not specified	Uncertain significance (Sep 26, 2022)
7-74822801-G-A		not specified	Uncertain significance (Jan 09, 2024)
7-74824959-A-G		not specified	Uncertain significance (Jun 07, 2023)
7-74824984-C-T		not specified	Uncertain significance (Sep 03, 2015)
7-74824988-T-C			Benign (Dec 31, 2019)
7-74825050-C-T		not specified	Uncertain significance (Jul 14, 2024)
7-74832834-G-A		not specified	Uncertain significance (Sep 16, 2021)
7-74836288-C-T			Likely benign (Mar 01, 2024)
7-74836311-A-C		not specified	Uncertain significance (Feb 22, 2023)
7-74836373-G-C			Likely benign (Jun 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GTF2IRD2	protein_coding	protein_coding	ENST00000405086	15	57365

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.15e-8	0.532	124159	3	210	124372	0.000857

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.12	260	316	0.823	0.0000193	6230
Missense in Polyphen		129	143.68	0.8978		2505
Synonymous	1.97	106	135	0.784	0.00000966	1768
Loss of Function	1.02	14	18.8	0.745	9.19e-7	489

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00146	0.00145
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000200	0.000198
Middle Eastern	0.000109	0.000109
South Asian	0.00464	0.00455
Other	0.000336	0.000327

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.121

Haploinsufficiency Scores

• ghis: 0.453

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.950

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gtf2ird2

Gene ontology

• Biological process: transition between fast and slow fiber
• Cellular component: nucleus
• Molecular function: DNA binding;protein binding