GTF2IRD2B

GTF2I repeat domain containing 2B

Basic information

Region (hg38): 7:75092573-75149817

Links

ENSG00000174428 ∙ NCBI:389524 ∙ OMIM:608900 ∙ HGNC:33125 ∙ Uniprot:Q6EKJ0 ∙ 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 GTF2IRD2B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GTF2IRD2B 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				1		1
missense			14	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	14	2	0

Variants in GTF2IRD2B

This is a list of pathogenic ClinVar variants found in the GTF2IRD2B region.

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

Position	Type	Phenotype	Significance	ClinVar
7-75108983-T-C		not specified	Uncertain significance (Dec 20, 2023)
7-75109010-T-C		not specified	Uncertain significance (Mar 01, 2023)
7-75109043-G-A		not specified	Likely benign (Apr 06, 2024)
7-75109047-C-G		not specified	Uncertain significance (May 26, 2024)
7-75112464-T-C		not specified	Uncertain significance (Jun 16, 2023)
7-75112506-C-T		not specified	Uncertain significance (Apr 12, 2022)
7-75120954-C-T		not specified	Uncertain significance (Nov 09, 2024)
7-75120959-G-A		not specified	Uncertain significance (May 27, 2022)
7-75120963-C-T		not specified	Uncertain significance (Jun 07, 2024)
7-75123199-C-T		not specified	Uncertain significance (Sep 16, 2021)
7-75123223-C-T		not specified	Uncertain significance (Dec 17, 2023)
7-75123232-T-C		not specified	Uncertain significance (Jan 19, 2025)
7-75123250-A-C		not specified	Uncertain significance (Sep 03, 2024)
7-75123505-A-G		not specified	Uncertain significance (Feb 19, 2025)
7-75135013-C-G		not specified	Uncertain significance (Aug 20, 2023)
7-75135022-G-A		not specified	Uncertain significance (Mar 03, 2022)
7-75136795-G-A			Likely benign (Mar 01, 2025)
7-75138964-T-A		not specified	Uncertain significance (Jan 12, 2024)
7-75149075-G-C			Likely benign (Mar 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GTF2IRD2B	protein_coding	protein_coding	ENST00000312575	15	57260

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0644	0.933	124360	0	8	124368	0.0000322

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.17	234	290	0.806	0.0000173	6208
Missense in Polyphen		98	134.35	0.72945		2824
Synonymous	-0.0140	125	125	1.00	0.00000884	1761
Loss of Function	2.62	5	16.5	0.304	7.80e-7	489

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000217	0.000217
Finnish	0.000100	0.0000924
European (Non-Finnish)	0.0000205	0.0000180
Middle Eastern	0.000217	0.000217
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0860

Haploinsufficiency Scores

• pHI: 0.166
• ghis: 0.454

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.192

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