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

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 16.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_001388453.1	NP_001375382.1	19	yes	-
ENST00000680821.2	ENSP00000504874.1	19	yes	-
NM_032134.3	NP_115510.2	19	-	-
ENST00000262765.10	ENSP00000262765.5	19	-	-

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.

• not_specified (257 variants)
• not_provided (35 variants)
• QRICH2-related_disorder (33 variants)
• Spermatogenic_failure_35 (8 variants)
• Asthenoteratozoospermia (1 variants)

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. These statistics are base on transcript: NM_001388453.1. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			6	24	6	36
missense			238	36	13	287
nonsense	4	1	2			7
start loss						0
frameshift		3				3
splice donor/acceptor (+/-2bp)		2	3			5
Total	4	6	249	60	19

Highest pathogenic variant AF is 0.00004708664

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
		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

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