SHQ1
Basic information
Region (hg38): 3:72749277-72861914
Links
Phenotypes
GenCC
Source:
- neurodevelopmental disorder with dystonia and seizures (Strong), mode of inheritance: AR
- neurodevelopmental disorder with dystonia and seizures (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Dystonia 35, childhood-onset | AR | Neurologic | The condition involves early-onset dystonia, and medical management (with L-DOPA) has been descriebd as beneficial | Neurologic | 29178645; 34542157 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (78 variants)
- not_provided (24 variants)
- Neurodevelopmental_disorder_with_dystonia_and_seizures (6 variants)
- SHQ1-related_disorder (3 variants)
- Dystonia_35,_childhood-onset (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SHQ1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000018130.3. 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 | 3 | |||||
missense | 81 | 96 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 4 | |||||
splice donor/acceptor (+/-2bp) | 1 | |||||
Total | 0 | 4 | 85 | 9 | 6 |
Highest pathogenic variant AF is 0.0011518738
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SHQ1 | protein_coding | protein_coding | ENST00000325599 | 11 | 112638 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
4.78e-11 | 0.352 | 125487 | 0 | 260 | 125747 | 0.00103 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.432 | 327 | 306 | 1.07 | 0.0000155 | 3770 |
Missense in Polyphen | 92 | 85.27 | 1.0789 | 1072 | ||
Synonymous | -0.0312 | 117 | 117 | 1.00 | 0.00000600 | 1095 |
Loss of Function | 1.04 | 19 | 24.6 | 0.773 | 0.00000133 | 291 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00112 | 0.00112 |
Ashkenazi Jewish | 0.000198 | 0.0000992 |
East Asian | 0.00110 | 0.00109 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.00164 | 0.00163 |
Middle Eastern | 0.00110 | 0.00109 |
South Asian | 0.000524 | 0.000523 |
Other | 0.000980 | 0.000978 |
dbNSFP
Source:
- Function
- FUNCTION: Required for the quantitative accumulation of H/ACA ribonucleoproteins (RNPs), including telomerase, probably through the stabilization of DKC1, from the time of its synthesis until its association with NOP10, NHP2, and NAF1 at the nascent H/ACA RNA. {ECO:0000269|PubMed:19383767}.;
Intolerance Scores
- loftool
- 0.907
- rvis_EVS
- 0.89
- rvis_percentile_EVS
- 89.19
Haploinsufficiency Scores
- pHI
- 0.108
- hipred
- Y
- hipred_score
- 0.550
- ghis
- 0.506
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.774
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Shq1
- Phenotype
Gene ontology
- Biological process
- box H/ACA snoRNP assembly;ribonucleoprotein complex assembly;positive regulation of apoptotic process;positive regulation of telomerase RNA localization to Cajal body;negative regulation of rRNA processing
- Cellular component
- nucleoplasm;nucleolus;cytoplasm;cytosol;Cajal body
- Molecular function
- protein binding;unfolded protein binding