PUDP

protein-coding

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

Gene summary

This gene encodes a member of the haloacid dehalogenase-like (HAD) hydrolase superfamily. The encoded protein has no known biological function. This gene has a pseudogene on chromosome 1. Multiple alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2010]

Previous symbols:

FAM16AX
HDHD1A
HDHD1

MANE transcript

NM_012080.5

Inheritance

—

ClinVar variants

U:60B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.36

Max pathogenic AF

—

Genomic locus

chrX:6,667,865-7,148,158

External References & Databases

Ensembl (ENSG00000130021)

Transcript & Mutation Effects

hg38 • Region Span ~480.3 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 PUDP variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 42

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_012080.5. 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			5 clinvar	3 clinvar		8
missense			50 clinvar	3 clinvar		53
nonsense			2 clinvar			2
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	60	6	0	66

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 21 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_012080.5	RefSeq	NP_036212.3	4	MANE Select
ENST00000381077.10	Ensembl	ENSP00000370467.6	4	MANE Select
NM_001135565.2	RefSeq	NP_001129037.1	5	Standard
NM_001178135.2	RefSeq	NP_001171606.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Metabolism of nucleotides
Metabolism
Pyrimidine salvage
Nucleotide salvage

Biological Process

biological_process
nucleotide metabolic process
dephosphorylation
pyrimidine nucleoside salvage

Molecular Function

magnesium ion binding
molecular_function
hydrolase activity
pseudouridine 5'-phosphatase activity

Cellular Component

cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000424830
Coding exons: 5
Length: 99271
Individuals with no LoFs: 119498
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 119500
p: 0.00000837

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0803	97	99.3	0.977	0.00000810	1626
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000088	0.000066	rare
Latino/Admixed American	0.000038	0.000030	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.153

Intolerance Scores

RVIS EVS: -0.1
RVIS percentile EVS: 46.49

Essentials

Essential (gene trap): N