GTF2H5

protein-coding

general 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]

Previous symbols:
  • C6orf175
  • TTD

MANE transcript

NM_207118.3

Inheritance

AR

ClinVar variants

P:10U:30B:17

Top phenotype

Trichothiodystrophy 3, photosensitive

gnomAD constraint

pLI —, LoF o/e 0.65

Max pathogenic AF

—

Genomic locus

chr6:158,168,350-158,199,344

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~31.0 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

trichothiodystrophy 3, photosensitiveSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014619

Submitter: Genomics England PanelApp

trichothiodystrophy 3, photosensitiveSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014619

Submitter: PanelApp Australia

trichothiodystrophy 3, photosensitiveSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014619

Submitter: Labcorp Genetics (formerly Invitae)

trichothiodystrophySUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0018053

Submitter: Orphanet

trichothiodystrophy 3, photosensitiveDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0014619

Submitter: G2P

Clinical Genomic Database (CGD)

Trichothiodystrophy 3, photosensitiveAR

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

Refs: 2189905; 8783572; 15220921; 18470933; 18603627Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GTF2H5 variants in ClinVar

6 Conditions Cataloged
not providedTotal: 55
Trichothiodystrophy 3, photosensitiveTotal: 8
Inborn genetic diseasesTotal: 8
not specifiedTotal: 2
GTF2H5-related disorderTotal: 1
GTF2H5-related disordersTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
17
clinvar
17
missense
2
clinvar
30
clinvar
32
nonsense
2
clinvar
1
clinvar
3
start loss
1
clinvar
1
clinvar
2
frameshift
2
clinvar
2
splice donor/acceptor (+/-2bp)
1
clinvar
1
Total733017057

Highest pathogenic variant AF is 0.000034706987

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 29 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_207118.3RefSeqNP_997001.12MANE Select
ENST00000607778.2EnsemblENSP00000476100.12MANE Select
ENST00000648328.1EnsemblENSP00000497338.12Standard
ENST00000648328.2EnsemblENSP00000497338.12Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-0.1234037.91.060.00000186470
Missense (PolyPhen)67.36920.8142124
Synonymous-0.3191715.41.108.63e-7133
Loss of Function0.57623.090.6462.15e-731

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American0.0000290.000029rare
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)0.0000970.000097rare
South Asian0.0000650.000065rare
Other00.0absent

dbNSFP Gene Annotations

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. 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

AllRecessiveDominant
MendelianMediumLowMedium
Primary ImmunodeficiencyMediumLowMedium
CancerMediumMediumMedium
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