PRPSAP1

phosphoribosyl pyrophosphate synthetase associated protein 1

Basic information

Region (hg38): 17:76309477-76384521

Links

ENSG00000161542 ∙ NCBI:5635 ∙ OMIM:601249 ∙ HGNC:9466 ∙ Uniprot:Q14558 ∙ 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 PRPSAP1 gene.

• Inborn genetic diseases (15 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRPSAP1 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			14	1		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	1	0

Variants in PRPSAP1

This is a list of pathogenic ClinVar variants found in the PRPSAP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-76311564-C-T		not specified	Uncertain significance (Sep 27, 2022)
17-76312877-A-G		not specified	Uncertain significance (Oct 04, 2022)
17-76312878-C-A		not specified	Uncertain significance (Oct 04, 2022)
17-76313008-A-C		not specified	Uncertain significance (Jan 23, 2023)
17-76328759-T-C		not specified	Uncertain significance (Sep 21, 2023)
17-76328774-G-A		not specified	Uncertain significance (Jan 10, 2023)
17-76328797-G-A		not specified	Uncertain significance (Jul 06, 2022)
17-76328830-C-T		not specified	Uncertain significance (May 04, 2022)
17-76330062-A-G		not specified	Uncertain significance (May 24, 2023)
17-76330068-C-G		not specified	Uncertain significance (Jun 24, 2022)
17-76330607-A-G		not specified	Uncertain significance (May 08, 2023)
17-76332268-T-C		not specified	Uncertain significance (Oct 24, 2023)
17-76332272-C-T		not specified	Uncertain significance (May 09, 2023)
17-76332312-C-A		not specified	Uncertain significance (Jan 12, 2024)
17-76353537-G-T		not specified	Uncertain significance (Jun 07, 2023)
17-76353562-A-C		not specified	Uncertain significance (Feb 13, 2024)
17-76353624-G-C		not specified	Likely benign (Oct 03, 2022)
17-76353634-G-C		not specified	Uncertain significance (Mar 16, 2022)
17-76353672-G-A		not specified	Likely benign (Oct 10, 2023)
17-76353697-T-C		not specified	Uncertain significance (Aug 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRPSAP1	protein_coding	protein_coding	ENST00000446526	10	75036

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.71e-7	0.424	125574	0	174	125748	0.000692

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.67	153	223	0.686	0.0000123	2491
Missense in Polyphen		42	65.119	0.64497		722
Synonymous	-1.25	100	85.3	1.17	0.00000529	771
Loss of Function	0.739	12	15.1	0.795	6.32e-7	213

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00326	0.00326
Ashkenazi Jewish	0.00	0.00
East Asian	0.000386	0.000381
Finnish	0.00	0.00
European (Non-Finnish)	0.000443	0.000422
Middle Eastern	0.000386	0.000381
South Asian	0.000299	0.000294
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Seems to play a negative regulatory role in 5- phosphoribose 1-diphosphate synthesis.

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.619
• rvis_EVS: -0.45
• rvis_percentile_EVS: 24

Haploinsufficiency Scores

• pHI: 0.0653
• hipred: N
• hipred_score: 0.349
• ghis: 0.628

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.930

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prpsap1

Gene ontology

• Biological process: 5-phosphoribose 1-diphosphate biosynthetic process;nucleobase-containing compound metabolic process;purine nucleotide biosynthetic process;nucleotide biosynthetic process;negative regulation of catalytic activity
• Cellular component: ribose phosphate diphosphokinase complex;cytoplasm
• Molecular function: magnesium ion binding;ribose phosphate diphosphokinase activity;enzyme inhibitor activity;protein binding;identical protein binding