PUDP

pseudouridine 5'-phosphatase, the group of HAD Asp-based non-protein phosphatases|Haloacid dehalogenase like hydrolase domain containing

Basic information

Region (hg38): X:6667864-7148158

Previous symbols: [ "FAM16AX", "HDHD1A", "HDHD1" ]

Links

ENSG00000130021 ∙ NCBI:8226 ∙ OMIM:306480 ∙ HGNC:16818 ∙ Uniprot:Q08623 ∙ 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 PUDP gene.

• Inborn genetic diseases (7 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PUDP 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				3		3
missense			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	7	4	0

Variants in PUDP

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

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

Position	Type	Phenotype	Significance	ClinVar
X-7050303-T-C		not specified	Uncertain significance (Dec 18, 2023)
X-7050367-T-C		not specified	Uncertain significance (Jun 22, 2021)
X-7057734-T-C			Likely benign (Feb 01, 2023)
X-7077257-C-T		not specified	Uncertain significance (Jan 17, 2024)
X-7077354-G-A		not specified	Uncertain significance (Jul 26, 2022)
X-7077369-C-T		not specified	Uncertain significance (Feb 12, 2024)
X-7077407-G-A		not specified	Uncertain significance (Sep 16, 2021)
X-7077423-G-A		not specified	Uncertain significance (Jan 16, 2024)
X-7077439-T-A		not specified	Uncertain significance (Oct 03, 2022)
X-7105630-C-T			Likely benign (Dec 01, 2022)
X-7105631-G-A		not specified	Uncertain significance (Apr 07, 2022)
X-7105669-T-C			Likely benign (Mar 01, 2023)
X-7105729-C-T			Likely benign (May 01, 2022)
X-7105790-T-G		not specified	Uncertain significance (Jun 27, 2022)
X-7105818-C-G		not specified	Uncertain significance (Jan 23, 2023)
X-7148071-T-C		not specified	Uncertain significance (Apr 25, 2022)
X-7148092-C-A		not specified	Uncertain significance (Jan 31, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PUDP	protein_coding	protein_coding	ENST00000424830	5	99271

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.127	0.788	119498	0	2	119500	0.00000837

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0803	97	99.3	0.977	0.00000810	1626
Missense in Polyphen		13	20.319	0.63981		367
Synonymous	-1.54	55	42.3	1.30	0.00000369	501
Loss of Function	1.38	2	5.48	0.365	3.45e-7	121

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000126	0.000104
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Dephosphorylates pseudouridine 5'-phosphate, a potential intermediate in rRNA degradation. Pseudouridine is then excreted intact in urine. {ECO:0000269|PubMed:20722631}.
• Pathway: Metabolism of nucleotides;Metabolism;Pyrimidine salvage;Nucleotide salvage (Consensus)

Recessive Scores

• pRec: 0.153

Intolerance Scores

• rvis_EVS: -0.1
• rvis_percentile_EVS: 46.49

Haploinsufficiency Scores

• pHI: 0.0718
• hipred: N
• hipred_score: 0.208
• ghis: 0.558

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Pudp

Gene ontology

• Biological process: biological_process;nucleotide metabolic process;dephosphorylation;pyrimidine nucleoside salvage
• Cellular component: cytosol
• Molecular function: magnesium ion binding;molecular_function;hydrolase activity;pseudouridine 5'-phosphatase activity