QRICH2

glutamine rich 2

Basic information

Region (hg38): 17:76274049-76308276

Links

ENSG00000129646 ∙ NCBI:84074 ∙ OMIM:618304 ∙ HGNC:25326 ∙ Uniprot:Q9H0J4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spermatogenic failure 35 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 35	AR	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	Genitourinary	30683861

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the QRICH2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the QRICH2 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				12	14	26
missense			89	15	22	126
nonsense						0
start loss						0
frameshift		1				1
inframe indel			1		2	3
splice donor/acceptor (+/-2bp)		1				1
splice region				2	1	3
non coding				2	3	5
Total	0	2	90	29	41

Variants in QRICH2

This is a list of pathogenic ClinVar variants found in the QRICH2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-76274109-C-A			Conflicting classifications of pathogenicity (Feb 01, 2023)
17-76274226-G-A		QRICH2-related disorder	Benign (Aug 30, 2024)
17-76274231-A-C		QRICH2-related disorder	Benign (Oct 28, 2019)
17-76275818-C-T		QRICH2-related disorder	Likely pathogenic (May 22, 2024)
17-76275850-C-T		QRICH2-related disorder	Likely benign (Jun 28, 2019)
17-76275857-C-T		not specified	Uncertain significance (Aug 02, 2021)
17-76275858-G-C		not specified	Uncertain significance (Dec 15, 2023)
17-76275929-C-T		not specified	Likely benign (Sep 27, 2021)
17-76275933-T-C		not specified	Uncertain significance (Feb 21, 2024)
17-76276688-C-T		not specified	Uncertain significance (Feb 15, 2023)
17-76276735-G-C		QRICH2-related disorder	Benign (Jun 27, 2019)
17-76276766-T-C		not specified	Likely benign (Oct 29, 2024)
17-76276769-T-C			Likely pathogenic (Sep 01, 2021)
17-76277201-C-G		not specified	Uncertain significance (Jan 02, 2024)
17-76277204-G-A		not specified	Uncertain significance (Jan 10, 2022)
17-76277218-G-A		QRICH2-related disorder	Benign (Nov 07, 2019)
17-76277246-G-A		not specified	Uncertain significance (Jun 07, 2024)
17-76277266-C-G		not specified	Uncertain significance (Mar 26, 2024)
17-76277266-C-T		not specified	Uncertain significance (Dec 01, 2022)
17-76277269-C-T		not specified	Uncertain significance (Sep 01, 2021)
17-76277991-T-C			Likely benign (Mar 01, 2023)
17-76277994-G-C		Spermatogenic failure 35	Pathogenic (Jul 31, 2020)
17-76278027-C-T			Likely benign (Sep 01, 2022)
17-76278035-G-A		not specified	Uncertain significance (May 05, 2023)
17-76278120-G-A		QRICH2-related disorder	Likely benign (Jun 19, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
QRICH2	protein_coding	protein_coding	ENST00000262765	19	33632

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.08e-28	0.146	125568	0	180	125748	0.000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.792	900	969	0.928	0.0000601	10724
Missense in Polyphen		246	262.48	0.93721		3079
Synonymous	0.681	342	358	0.954	0.0000207	3429
Loss of Function	2.02	54	72.6	0.744	0.00000395	778

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00319	0.00319
Ashkenazi Jewish	0.00	0.00
East Asian	0.000604	0.000598
Finnish	0.000232	0.000231
European (Non-Finnish)	0.000743	0.000739
Middle Eastern	0.000604	0.000598
South Asian	0.000564	0.000555
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0694

Intolerance Scores

• loftool: 0.985
• rvis_EVS: 1.67
• rvis_percentile_EVS: 96.32

Haploinsufficiency Scores

• pHI: 0.127
• hipred: N
• hipred_score: 0.145
• ghis: 0.424

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0594

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Qrich2