GTF2H1

general transcription factor IIH subunit 1, the group of Nucleotide excision repair|General transcription factor IIH complex subunits

Basic information

Region (hg38): 11:18322294-18367045

Links

ENSG00000110768 ∙ NCBI:2965 ∙ OMIM:189972 ∙ HGNC:4655 ∙ Uniprot:P32780 ∙ 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 GTF2H1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GTF2H1 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			25	1		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	1	1

Variants in GTF2H1

This is a list of pathogenic ClinVar variants found in the GTF2H1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-18333207-C-T		not specified	Uncertain significance (Aug 02, 2021)
11-18335818-C-A		not specified	Uncertain significance (Jan 23, 2023)
11-18335822-A-G		not specified	Uncertain significance (May 05, 2023)
11-18335841-A-G		not specified	Uncertain significance (Jan 25, 2023)
11-18335844-A-G		not specified	Uncertain significance (Oct 27, 2022)
11-18335847-G-A		not specified	Uncertain significance (Dec 19, 2023)
11-18335872-A-G			Benign (Apr 11, 2018)
11-18338251-G-C		not specified	Uncertain significance (Jan 03, 2024)
11-18341354-G-A		not specified	Uncertain significance (Oct 16, 2023)
11-18341391-T-G		not specified	Uncertain significance (Oct 12, 2022)
11-18341587-G-A		not specified	Uncertain significance (Feb 12, 2024)
11-18341596-C-A		not specified	Uncertain significance (Jun 26, 2023)
11-18347588-G-A		not specified	Uncertain significance (Jan 04, 2024)
11-18347649-A-G		not specified	Uncertain significance (Jan 03, 2024)
11-18347879-A-G		not specified	Uncertain significance (Mar 20, 2024)
11-18347891-C-G		not specified	Uncertain significance (May 24, 2023)
11-18351935-A-C		not specified	Uncertain significance (Jun 02, 2023)
11-18351939-C-T		not specified	Uncertain significance (Dec 07, 2023)
11-18351968-A-G		not specified	Uncertain significance (Oct 12, 2021)
11-18352386-T-G		not specified	Uncertain significance (Dec 13, 2022)
11-18352424-C-T		not specified	Uncertain significance (Aug 21, 2023)
11-18358006-G-T		not specified	Uncertain significance (Jan 26, 2022)
11-18358007-C-T		not specified	Uncertain significance (Jan 26, 2022)
11-18358024-A-G		not specified	Uncertain significance (Oct 03, 2022)
11-18358547-A-C		not specified	Uncertain significance (Mar 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GTF2H1	protein_coding	protein_coding	ENST00000265963	14	44750

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.990	0.0102	125737	0	8	125745	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.80	202	288	0.702	0.0000145	3629
Missense in Polyphen		24	68.642	0.34964		940
Synonymous	0.202	97	99.6	0.974	0.00000481	997
Loss of Function	4.53	4	31.4	0.127	0.00000170	376

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000620	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000544	0.0000527
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the general transcription and DNA repair factor IIH (TFIIH) core complex, which is involved in general and transcription-coupled nucleotide excision repair (NER) of damaged DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. In NER, TFIIH acts by opening DNA around the lesion to allow the excision of the damaged oligonucleotide and its replacement by a new DNA fragment. In transcription, TFIIH has an essential role in transcription initiation. When the pre- initiation complex (PIC) has been established, TFIIH is required for promoter opening and promoter escape. Phosphorylation of the C-terminal tail (CTD) of the largest subunit of RNA polymerase II by the kinase module CAK controls the initiation of transcription. {ECO:0000269|PubMed:9852112}.
• Pathway: Nucleotide excision repair - Homo sapiens (human);Basal transcription factors - Homo sapiens (human);Viral carcinogenesis - Homo sapiens (human);Eukaryotic Transcription Initiation;DNA Repair;Disease;RNA Pol II CTD phosphorylation and interaction with CE during HIV infection;NoRC negatively regulates rRNA expression;Negative epigenetic regulation of rRNA expression;Formation of the HIV-1 Early Elongation Complex;Epigenetic regulation of gene expression;Gene expression (Transcription);Formation of HIV-1 elongation complex containing HIV-1 Tat;Tat-mediated elongation of the HIV-1 transcript;HIV Transcription Elongation;Formation of HIV elongation complex in the absence of HIV Tat;Generic Transcription Pathway;Transcription of the HIV genome;Late Phase of HIV Life Cycle;HIV Life Cycle;HIV Infection;RNA Polymerase II HIV Promoter Escape;RNA Polymerase II Pre-transcription Events;RNA Polymerase II Transcription Initiation;RNA Polymerase II Transcription Initiation And Promoter Clearance;RNA Pol II CTD phosphorylation and interaction with CE;Formation of RNA Pol II elongation complex ;RNA Polymerase I Promoter Clearance;HIV Transcription Initiation;RNA Polymerase II Transcription;Metabolism of RNA;Infectious disease;RNA Polymerase I Transcription Termination;RNA Polymerase I Transcription;RNA Polymerase II Transcription Elongation;RNA Polymerase I Transcription Initiation;RNA Polymerase I Promoter Escape;RNA Polymerase II Promoter Escape;RNA Polymerase I Chain Elongation;AndrogenReceptor;RNA Polymerase II Transcription Pre-Initiation And Promoter Opening;TP53 Regulates Transcription of DNA Repair Genes;Transcriptional Regulation by TP53;mRNA Capping;Formation of the Early Elongation Complex;Formation of Incision Complex in GG-NER;Dual Incision in GG-NER;Global Genome Nucleotide Excision Repair (GG-NER);Formation of TC-NER Pre-Incision Complex;Dual incision in TC-NER;Gap-filling DNA repair synthesis and ligation in TC-NER;Transcription-Coupled Nucleotide Excision Repair (TC-NER);Nucleotide Excision Repair (Consensus)

Recessive Scores

• pRec: 0.159

Intolerance Scores

• loftool: 0.571
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.69

Haploinsufficiency Scores

• pHI: 0.906
• hipred: Y
• hipred_score: 0.793
• ghis: 0.630

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.996

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gtf2h1

Gene ontology

• Biological process: regulation of cyclin-dependent protein serine/threonine kinase activity;DNA repair;transcription-coupled nucleotide-excision repair;nucleotide-excision repair, preincision complex stabilization;nucleotide-excision repair, preincision complex assembly;nucleotide-excision repair, DNA incision, 5'-to lesion;transcription by RNA polymerase I;transcription initiation from RNA polymerase I promoter;termination of RNA polymerase I transcription;transcription by RNA polymerase II;transcription initiation from RNA polymerase II promoter;transcription elongation from RNA polymerase II promoter;7-methylguanosine mRNA capping;nucleotide-excision repair, DNA incision;positive regulation of transcription by RNA polymerase II;phosphorylation of RNA polymerase II C-terminal domain;global genome nucleotide-excision repair
• Cellular component: transcription factor TFIIH core complex;nucleoplasm;transcription factor TFIIH holo complex
• Molecular function: chromatin binding;protein kinase activity;protein binding;DNA-dependent ATPase activity;RNA polymerase II CTD heptapeptide repeat kinase activity