QRICH1

glutamine rich 1, the group of Caspase recruitment domain containing

Basic information

Region (hg38): 3:49029707-49094363

Links

ENSG00000198218 ∙ NCBI:54870 ∙ OMIM:617387 ∙ HGNC:24713 ∙ Uniprot:Q2TAL8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown
• Ververi-Brady syndrome (Moderate), mode of inheritance: AD
• Ververi-Brady syndrome (Definitive), mode of inheritance: AD
• Ververi-Brady syndrome (Strong), mode of inheritance: AD
• syndromic intellectual disability (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Ververi-Brady syndrome	AD	General	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	Craniofacial; Musculoskeletal; Neurologic	28692176; 30281152

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the QRICH1 gene.

• Ververi-Brady syndrome (22 variants)
• not provided (8 variants)
• Inborn genetic diseases (5 variants)
• Intellectual disability (2 variants)
• Intellectual disability, mild (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the QRICH1 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				11	1	12
missense		9	52	1	1	63
nonsense	14	1				15
start loss						0
frameshift	13	7				20
inframe indel			1			1
splice donor/acceptor (+/-2bp)	2	1	1			4
splice region				1		1
non coding			1			1
Total	29	18	55	12	2

Variants in QRICH1

This is a list of pathogenic ClinVar variants found in the QRICH1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-49030501-CTT-C		Ververi-Brady syndrome	Likely pathogenic (Jan 19, 2023)
3-49030517-G-A		Inborn genetic diseases	Conflicting classifications of pathogenicity (Sep 25, 2023)
3-49030518-C-T		QRICH1-related disorder	Benign (May 20, 2019)
3-49030519-G-A		Inborn genetic diseases	Uncertain significance (Aug 10, 2023)
3-49030526-T-C			Uncertain significance (Jan 19, 2022)
3-49030535-T-C		Inborn genetic diseases	Uncertain significance (Jun 11, 2021)
3-49030554-C-G		QRICH1-related disorder	Uncertain significance (Oct 11, 2023)
3-49030567-C-T		Ververi-Brady syndrome	Conflicting classifications of pathogenicity (Dec 21, 2021)
3-49030569-G-C		Ververi-Brady syndrome	Uncertain significance (Dec 09, 2021)
3-49030574-G-T		QRICH1-related disorder	Uncertain significance (Sep 25, 2024)
3-49030576-C-T		Ververi-Brady syndrome	Likely pathogenic (Dec 21, 2021)
3-49030608-G-C			Uncertain significance (May 27, 2022)
3-49030617-G-A		QRICH1-related disorder	Benign/Likely benign (Jul 01, 2024)
3-49030624-C-T		Ververi-Brady syndrome	Likely pathogenic (Oct 17, 2023)
3-49030661-T-G		not specified	Uncertain significance (Nov 04, 2022)
3-49032207-A-C			Uncertain significance (Jul 29, 2022)
3-49032241-T-C			Uncertain significance (Jan 21, 2022)
3-49032245-C-T			Likely benign (Aug 01, 2023)
3-49032255-G-C			Uncertain significance (Nov 01, 2023)
3-49032664-G-A			Uncertain significance (Mar 26, 2022)
3-49032671-C-T			Likely benign (Jan 01, 2024)
3-49032688-G-A		Ververi-Brady syndrome	Uncertain significance (Jan 29, 2019)
3-49032698-GTTC-G			Uncertain significance (Feb 14, 2023)
3-49032705-T-C			Uncertain significance (Apr 01, 2023)
3-49032715-G-A		Ververi-Brady syndrome • Intellectual disability	Pathogenic (Dec 21, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
QRICH1	protein_coding	protein_coding	ENST00000395443	9	64657

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.996	0.00424	125741	0	6	125747	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.71	211	427	0.495	0.0000230	5050
Missense in Polyphen		38	101.39	0.37478		1229
Synonymous	-0.470	178	170	1.05	0.00000962	1566
Loss of Function	4.98	5	38.2	0.131	0.00000188	388

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000910	0.0000910
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000552	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000266	0.0000264
Middle Eastern	0.0000552	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0751

Intolerance Scores

• loftool: 0.0214
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.25

Haploinsufficiency Scores

• pHI: 0.306
• hipred: Y
• hipred_score: 0.673
• ghis: 0.572

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.754

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Qrich1
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; digestive/alimentary phenotype; renal/urinary system phenotype; immune system phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; craniofacial phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;biological_process;regulation of cell morphogenesis
• Cellular component: cellular_component;nucleus;nucleoplasm
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;molecular_function;protein binding