PYURF

protein-coding

PIGY upstream open reading frame

Gene summary

The product of this gene, which is well-conserved, is encoded by the same bicistronic transcript that encodes phosphatidylinositol glycan anchor biosynthesis, class Y, but the two proteins are unrelated. This gene represents the protein encoded by the upstream open reading frame, while the protein encoded by the downstream open reading frame is represented by GeneID:84992. [provided by RefSeq, Aug 2012]

MANE transcript

NM_032906.5

Inheritance

—

ClinVar variants

P:1U:2

Top phenotype

Hyperphosphatasia with intellectual disability syndrome 6

gnomAD constraint

pLI —, LoF o/e 0.45

Max pathogenic AF

—

Genomic locus

chr4:88,520,998-88,523,776

External References & Databases

Ensembl (ENSG00000145337)

NCBI Gene (100996939)

Transcript & Mutation Effects

hg38 • Region Span ~2.8 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 PYURF variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 1

Hyperphosphatasia with intellectual disability syndrome 6Total: 1

Mitochondrial diseaseTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032906.5. 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						0
missense			2 clinvar			2
nonsense						0
start loss						0
frameshift	1 clinvar					1
splice donor/acceptor (+/-2bp)						0
Total	1	0	2	0	0	3

Highest pathogenic variant AF is 7.1463484e-7

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032906.5	RefSeq	NP_116295.1	2	MANE Select
ENST00000273968.5	Ensembl	ENSP00000273968.4	2	MANE Select
ENST00001135370.1	Ensembl	ENSP00000804176.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

GPI anchor biosynthetic process
positive regulation of metabolic process

Molecular Function

protein binding

Cellular Component

glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex
mitochondrion
endoplasmic reticulum membrane
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000273968
Coding exons: 2
Length: 2829
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.387	55	63.7	0.864	0.00000322	713
Missense (PolyPhen)		9	16.561	0.54344		235
Synonymous	1.10	19	26.2	0.726	0.00000121	242
Loss of Function	0.763	1	2.23	0.448	9.20e-8	39

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N

Gene Damage Prediction

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