PRPSAP1

protein-coding

phosphoribosyl pyrophosphate synthetase associated protein 1

Gene summary

Enables identical protein binding activity. Predicted to be involved in 5-phosphoribose 1-diphosphate biosynthetic process and purine nucleotide biosynthetic process. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_002766.3

Inheritance

—

ClinVar variants

U:45B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.79

Max pathogenic AF

—

Genomic locus

chr17:76,309,478-76,384,521

External References & Databases

Ensembl (ENSG00000161542)

Transcript & Mutation Effects

hg38 • Region Span ~75.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PRPSAP1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 41

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002766.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	1 clinvar		2
missense			41 clinvar	3 clinvar		44
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	45	4	0	49

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 32 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002766.3	RefSeq	NP_002757.2	10	MANE Select
ENST00000446526.8	Ensembl	ENSP00000414624.2	10	MANE Select
NM_001330503.2	RefSeq	NP_001317432.1	7	Standard
NM_001366236.2	RefSeq	NP_001353165.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

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

Molecular Function

magnesium ion binding
ribose phosphate diphosphokinase activity
enzyme inhibitor activity
protein binding
identical protein binding

Cellular Component

ribose phosphate diphosphokinase complex
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000446526
Coding exons: 10
Length: 75036
Individuals with no LoFs: 125574
Homozygous LoFs: 0
Heterozygous LoFs: 174
Defined: 125748
p: 0.000692

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.67	153	223	0.686	0.0000123	2491
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.0031	0.0030	notable
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00039	0.00038	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00044	0.00042	rare
South Asian	0.00030	0.00029	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.930

Gene Damage Prediction

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