GTF2H5
protein-codinggeneral transcription factor IIH subunit 5, the group of General transcription factor IIH complex subunits|Nucleotide excision repair
Gene summary
This gene encodes a subunit of transcription/repair factor TFIIH, which functions in gene transcription and DNA repair. This protein stimulates ERCC3/XPB ATPase activity to trigger DNA opening during DNA repair, and is implicated in regulating cellular levels of TFIIH. Mutations in this gene result in trichothiodystrophy, complementation group A. [provided by RefSeq, Mar 2009]
- C6orf175
- TTD
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~31.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0014619
Submitter: Genomics England PanelApp
Inheritance Pattern: AR
Disease ID:MONDO:0014619
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0014619
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0018053
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0014619
Submitter: G2P
Clinical Genomic Database (CGD)
Manifestation: Dermatologic; Musculoskeletal; Neurologic; Ophthalmologic
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to GTF2H5 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_207118.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 17 | 17 | ||||
| missense | 2 | 30 | 32 | |||
| nonsense | 2 | 1 | 3 | |||
| start loss | 1 | 1 | 2 | |||
| frameshift | 2 | 2 | ||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 7 | 3 | 30 | 17 | 0 | 57 |
Highest pathogenic variant AF is 0.000034706987
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_997001.1 | 2 | MANE Select | |
| Ensembl | ENSP00000476100.1 | 2 | MANE Select | |
| Ensembl | ENSP00000497338.1 | 2 | Standard | |
| Ensembl | ENSP00000497338.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Nucleotide excision repair - Homo sapiens (human)
- Basal transcription factors - Homo sapiens (human)
- DNA Repair
- Disease
- RNA Pol II CTD phosphorylation and interaction with CE during HIV infection
Biological Process
- transcription-coupled nucleotide-excision repair
- nucleotide-excision repair
- nucleotide-excision repair, preincision complex stabilization
- nucleotide-excision repair, preincision complex assembly
- nucleotide-excision repair, DNA incision, 5'-to lesion
Molecular Function
- rDNA binding
- protein binding
Cellular Component
- transcription factor TFIIH core complex
- nucleoplasm
- transcription factor TFIID complex
- transcription factor TFIIH holo complex
- nucleolus
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000607778
- Coding exons
- 2
- Length
- 30993
- Individuals with no LoFs
- 125729
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 14
- Defined
- 125743
- p
- 0.0000557
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.123 | 40 | 37.9 | 1.06 | 0.00000186 | 470 |
| Missense (PolyPhen) | 6 | 7.3692 | 0.8142 | 124 | ||
| Synonymous | -0.319 | 17 | 15.4 | 1.10 | 8.63e-7 | 133 |
| Loss of Function | 0.576 | 2 | 3.09 | 0.646 | 2.15e-7 | 31 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000097 | 0.000097 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- 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. Necessary for the stability of the TFIIH complex and for the presence of normal levels of TFIIH in the cell. {ECO:0000269|PubMed:15220921}.;
- Disease
- DISEASE: Trichothiodystrophy 3, photosensitive (TTD3) [MIM:616395]: A form of trichothiodystrophy, an autosomal recessive disease characterized by sulfur-deficient brittle hair and multisystem variable abnormalities. The spectrum of clinical features varies from mild disease with only hair involvement to severe disease with cutaneous, neurologic and profound developmental defects. Ichthyosis, intellectual and developmental disabilities, decreased fertility, abnormal characteristics at birth, ocular abnormalities, short stature, and infections are common manifestations. There are both photosensitive and non- photosensitive forms of the disorder. {ECO:0000269|PubMed:15220921}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.186
Intolerance Scores
- LoFtool
- 0.517
- RVIS EVS
- -0.08
- RVIS percentile EVS
- 47.79
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Indispensability pred.
- E
- Indispensability score
- 0.973
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Medium |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Medium | Medium |