SHQ1

SHQ1, H/ACA ribonucleoprotein assembly factor

Basic information

Region (hg38): 3:72749276-72861914

Links

ENSG00000144736 ∙ NCBI:55164 ∙ OMIM:613663 ∙ HGNC:25543 ∙ Uniprot:Q6PI26 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• neurodevelopmental disorder with dystonia and seizures (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

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 ClinVar and linked to the SHQ1 gene.

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.

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					2	2
missense		1	36	4	4	45
nonsense						0
start loss						0
frameshift			2			2
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region			1	1		2
non coding						0
Total	0	1	39	4	6

Variants in SHQ1

This is a list of pathogenic ClinVar variants found in the SHQ1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-72750308-G-GTC		SHQ1-related disorder	Uncertain significance (Nov 08, 2023)
3-72750330-C-T		not specified	Likely benign (Sep 14, 2022)
3-72750331-G-A		not specified	Uncertain significance (Mar 29, 2024)
3-72750343-T-G			Uncertain significance (Jan 24, 2023)
3-72750397-C-T			Benign (Apr 30, 2018)
3-72750405-A-C		not specified	Uncertain significance (Jun 22, 2023)
3-72750438-G-A		not specified	Uncertain significance (Dec 08, 2023)
3-72750490-G-A		not specified	Likely benign (Dec 19, 2022)
3-72750498-C-T		not specified	Uncertain significance (Mar 25, 2024)
3-72750535-A-C		not specified	Uncertain significance (Oct 30, 2023)
3-72750540-C-A		not specified	Uncertain significance (Jan 03, 2022)
3-72750556-C-A		not specified	Uncertain significance (May 31, 2023)
3-72750622-A-G		not specified	Uncertain significance (May 22, 2023)
3-72750648-G-A		not specified	Uncertain significance (Jan 02, 2024)
3-72750784-T-C		not specified	Uncertain significance (Aug 15, 2023)
3-72750792-G-C		not specified	Uncertain significance (Nov 09, 2021)
3-72750834-G-A		not specified	Uncertain significance (May 08, 2024)
3-72792982-T-C		not specified	Uncertain significance (Oct 26, 2022)
3-72812680-A-G			Benign (Sep 12, 2018)
3-72812734-G-C		Neurodevelopmental disorder with dystonia and seizures	Likely pathogenic (Jan 23, 2024)
3-72812797-G-C			Uncertain significance (May 18, 2023)
3-72817217-TACATGCACTTA-T		SHQ1-related disorder	Uncertain significance (Jan 04, 2024)
3-72817238-C-T		Neurodevelopmental disorder with dystonia and seizures	Pathogenic (Jun 23, 2022)
3-72817253-G-A		not specified	Uncertain significance (May 14, 2024)
3-72817261-T-C			Uncertain significance (Jun 21, 2023)

GnomAD

Source: gnomAD

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: dbNSFP

• 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

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