PRPSAP2

phosphoribosyl pyrophosphate synthetase associated protein 2

Basic information

Region (hg38): 17:18840085-18931287

Links

ENSG00000141127 ∙ NCBI:5636 ∙ OMIM:603762 ∙ HGNC:9467 ∙ Uniprot:O60256 ∙ 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 PRPSAP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRPSAP2 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			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	0

Variants in PRPSAP2

This is a list of pathogenic ClinVar variants found in the PRPSAP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-18865884-A-C		not specified	Uncertain significance (Dec 18, 2023)
17-18877784-C-T		not specified	Uncertain significance (Sep 13, 2023)
17-18889849-G-A		not specified	Uncertain significance (Dec 20, 2023)
17-18911224-G-T		not specified	Uncertain significance (Oct 06, 2023)
17-18928872-G-A		not specified	Uncertain significance (Feb 05, 2024)
17-18930553-A-G		not specified	Uncertain significance (Mar 01, 2024)
17-18930561-C-A		not specified	Uncertain significance (Nov 03, 2023)
17-18930667-A-G		not specified	Uncertain significance (Sep 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRPSAP2	protein_coding	protein_coding	ENST00000268835	10	91184

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00312	0.987	125732	0	15	125747	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.60	106	213	0.498	0.0000117	2420
Missense in Polyphen		20	50.117	0.39907		542
Synonymous	0.332	73	76.7	0.952	0.00000437	709
Loss of Function	2.25	7	17.0	0.411	7.15e-7	233

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000126	0.000126
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000666	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000803	0.0000791
Middle Eastern	0.0000666	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.0874

Intolerance Scores

• loftool: 0.377
• rvis_EVS: -0.23
• rvis_percentile_EVS: 37.11

Haploinsufficiency Scores

• pHI: 0.0736
• hipred: Y
• hipred_score: 0.592
• ghis: 0.574

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.257

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prpsap2
• Phenotype: limbs/digits/tail phenotype; skeleton phenotype

Gene ontology

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