QPRT

quinolinate phosphoribosyltransferase

Basic information

Region (hg38): 16:29663278-29698699

Links

ENSG00000103485 ∙ NCBI:23475 ∙ OMIM:606248 ∙ HGNC:9755 ∙ Uniprot:Q15274 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

• Inborn genetic diseases (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the QPRT 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						0
missense			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	0

Variants in QPRT

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

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

Position	Type	Phenotype	Significance	ClinVar
16-29663755-G-T		SPN-related disorder	Likely benign (Apr 25, 2019)
16-29663770-C-A		not specified	Uncertain significance (Sep 13, 2023)
16-29663793-C-T		SPN-related disorder	Benign (Mar 03, 2020)
16-29663921-C-G		not specified	Uncertain significance (Jan 10, 2023)
16-29663985-G-A		not specified	Uncertain significance (Feb 15, 2023)
16-29664005-A-G		SPN-related disorder	Benign (May 23, 2019)
16-29664050-G-A		not specified	Uncertain significance (Jan 26, 2023)
16-29664115-C-G		SPN-related disorder	Likely benign (Apr 20, 2023)
16-29664152-A-G		not specified	Uncertain significance (Feb 22, 2023)
16-29664186-C-T		not specified	Likely benign (Aug 30, 2021)
16-29664202-G-A		SPN-related disorder	Likely benign (Mar 22, 2019)
16-29664210-C-T		not specified	Uncertain significance (Feb 28, 2023)
16-29664354-C-T		not specified	Uncertain significance (Dec 07, 2021)
16-29664376-C-T		SPN-related disorder	Benign (Apr 10, 2019)
16-29664380-G-A		not specified	Likely benign (Jan 23, 2024)
16-29664394-G-C		not specified	Uncertain significance (Aug 02, 2021)
16-29664403-C-G		SPN-related disorder	Likely benign (Feb 07, 2022)
16-29664403-C-T			Benign (May 16, 2018)
16-29664420-T-C		not specified	Uncertain significance (Jul 21, 2021)
16-29664525-C-T			Benign (Jul 31, 2018)
16-29664565-G-A			Benign (Aug 20, 2018)
16-29664579-G-A		not specified	Uncertain significance (Dec 21, 2022)
16-29664607-C-T		SPN-related disorder	Benign (Oct 21, 2019)
16-29664608-G-A		not specified	Uncertain significance (Sep 13, 2023)
16-29664620-G-C		not specified	Uncertain significance (Aug 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
QPRT	protein_coding	protein_coding	ENST00000395384	4	35421

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00470	0.888	125666	0	39	125705	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.12	148	192	0.772	0.0000123	1868
Missense in Polyphen		67	87.384	0.76673		893
Synonymous	0.0669	96	96.8	0.991	0.00000727	681
Loss of Function	1.37	5	9.58	0.522	4.95e-7	97

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000239	0.000214
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000633	0.0000616
Middle Eastern	0.000111	0.000109
South Asian	0.000793	0.000784
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the catabolism of quinolinic acid (QA). {ECO:0000269|PubMed:17868694}.
• Pathway: Nicotinate and nicotinamide metabolism - Homo sapiens (human);Nicotinate and Nicotinamide Metabolism;NAD Biosynthesis II (from tryptophan);NAD+ biosynthetic pathways;Metabolism;Nicotinate Nicotinamide metabolism;Nicotinate metabolism;Metabolism of water-soluble vitamins and cofactors;Metabolism of vitamins and cofactors;NAD biosynthesis from 2-amino-3-carboxymuconate semialdehyde;NAD <i>de novo</i> biosynthesis;Tryptophan degradation;superpathway of tryptophan utilization (Consensus)

Recessive Scores

• pRec: 0.179

Intolerance Scores

• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.73

Haploinsufficiency Scores

• pHI: 0.180
• hipred: N
• hipred_score: 0.312
• ghis: 0.416

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.964

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Qprt

Gene ontology

• Biological process: NAD biosynthetic process;NAD metabolic process;quinolinate catabolic process;protein complex oligomerization
• Cellular component: cytoplasm;cytosol;extracellular exosome
• Molecular function: nicotinate-nucleotide diphosphorylase (carboxylating) activity;protein binding;protein homodimerization activity