THOC6
Basic information
Region (hg38): 16:3024027-3027755
Previous symbols: [ "WDR58" ]
Links
Phenotypes
GenCC
Source:
- THOC6-related developmental delay-microcephaly-facial dysmorphism syndrome (Definitive), mode of inheritance: AR
- THOC6-related developmental delay-microcephaly-facial dysmorphism syndrome (Supportive), mode of inheritance: AR
- THOC6-related developmental delay-microcephaly-facial dysmorphism syndrome (Moderate), mode of inheritance: AR
- THOC6-related developmental delay-microcephaly-facial dysmorphism syndrome (Strong), mode of inheritance: AR
- THOC6-related developmental delay-microcephaly-facial dysmorphism syndrome (Definitive), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Beaulieu-Boycott-Innes syndrome | AR | Cardiovascular | The condition can involve congenital cardiac anomalies, and awareness may allow early management | Cardiovascular; Craniofacial; Dental; Genitourinary; Neurologic; Renal | 23621916; 26739162; 27102954; 30476144 |
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn_genetic_diseases (62 variants)
- not_provided (30 variants)
- THOC6-related_developmental_delay-microcephaly-facial_dysmorphism_syndrome (29 variants)
- THOC6-related_disorder (8 variants)
- Intellectual_disability (4 variants)
- Dystonia,_early-onset,_and/or_spastic_paraplegia (3 variants)
- not_specified (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the THOC6 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000024339.5. Only rare variants are included in the table.
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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 15 | 17 | ||||
missense | 62 | 70 | ||||
nonsense | 9 | |||||
start loss | 0 | |||||
frameshift | 6 | |||||
splice donor/acceptor (+/-2bp) | 6 | |||||
Total | 11 | 14 | 64 | 17 | 2 |
Highest pathogenic variant AF is 0.000364347
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
THOC6 | protein_coding | protein_coding | ENST00000326266 | 13 | 3729 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.000478 | 0.998 | 125714 | 0 | 34 | 125748 | 0.000135 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.402 | 223 | 207 | 1.08 | 0.0000128 | 2189 |
Missense in Polyphen | 54 | 55.926 | 0.96557 | 646 | ||
Synonymous | -1.47 | 101 | 83.9 | 1.20 | 0.00000527 | 697 |
Loss of Function | 2.81 | 10 | 25.2 | 0.397 | 0.00000131 | 256 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000187 | 0.000185 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000489 | 0.000489 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.000150 | 0.000149 |
Middle Eastern | 0.000489 | 0.000489 |
South Asian | 0.000132 | 0.000131 |
Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Acts as component of the THO subcomplex of the TREX complex which is thought to couple mRNA transcription, processing and nuclear export, and which specifically associates with spliced mRNA and not with unspliced pre-mRNA. TREX is recruited to spliced mRNAs by a transcription-independent mechanism, binds to mRNA upstream of the exon-junction complex (EJC) and is recruited in a splicing- and cap-dependent manner to a region near the 5' end of the mRNA where it functions in mRNA export to the cytoplasm via the TAP/NFX1 pathway. The TREX complex is essential for the export of Kaposi's sarcoma-associated herpesvirus (KSHV) intronless mRNAs and infectious virus production. Plays a role in apoptosis negative control involved in brain development. {ECO:0000269|PubMed:15833825, ECO:0000269|PubMed:15998806, ECO:0000269|PubMed:17190602, ECO:0000269|PubMed:18974867, ECO:0000269|PubMed:23621916}.;
- Disease
- DISEASE: Beaulieu-Boycott-Innes syndrome (BBIS) [MIM:613680]: An autosomal recessive neurodevelopmental disorder characterized by delayed development, moderate intellectual disability, and dysmorphic facial features. Other developmental anomalies, such as cardiac and renal defects, may also occur. {ECO:0000269|PubMed:23621916}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- RNA transport - Homo sapiens (human);Gene expression (Transcription);RNA Polymerase II Transcription;Metabolism of RNA;Cleavage of Growing Transcript in the Termination Region ;RNA Polymerase II Transcription Termination;Transport of Mature mRNA derived from an Intron-Containing Transcript;mRNA 3,-end processing;Transport of Mature Transcript to Cytoplasm;Processing of Capped Intron-Containing Pre-mRNA
(Consensus)
Recessive Scores
- pRec
- 0.110
Intolerance Scores
- loftool
- 0.904
- rvis_EVS
- -1.11
- rvis_percentile_EVS
- 6.72
Haploinsufficiency Scores
- pHI
- 0.250
- hipred
- Y
- hipred_score
- 0.528
- ghis
- 0.595
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.758
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Thoc6
- Phenotype
Gene ontology
- Biological process
- RNA export from nucleus;mRNA export from nucleus;apoptotic process;central nervous system development;RNA splicing;mRNA 3'-end processing;negative regulation of apoptotic process;viral mRNA export from host cell nucleus
- Cellular component
- transcription export complex;THO complex;THO complex part of transcription export complex;nuclear chromosome, telomeric region;nucleus;nucleoplasm;nuclear body;nuclear speck
- Molecular function
- RNA binding