PYURF

PIGY upstream open reading frame

Basic information

Region (hg38): 4:88520997-88523776

Links

ENSG00000145337 ∙ NCBI:100996939 ∙ OMIM:619956 ∙ HGNC:44317 ∙ Uniprot:Q96I23 ∙ 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 PYURF gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PYURF 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					1	1
missense			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			7	4		11
Total	0	0	9	4	1

Variants in PYURF

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

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

Position	Type	Phenotype	Significance	ClinVar
4-88521628-A-G			Likely benign (Dec 01, 2023)
4-88521639-T-C		Hyperphosphatasia with intellectual disability syndrome 6	Uncertain significance (Dec 09, 2023)
4-88521647-G-A			Likely benign (Feb 22, 2023)
4-88521653-A-G		Hyperphosphatasia with intellectual disability syndrome 6	Pathogenic (Dec 19, 2022)
4-88521680-G-C			Uncertain significance (Sep 27, 2022)
4-88521682-G-C			Uncertain significance (Sep 18, 2023)
4-88521689-C-T		Hyperphosphatasia with intellectual disability syndrome 6	Uncertain significance (Dec 07, 2018)
4-88521744-A-G			Uncertain significance (Apr 20, 2023)
4-88521769-C-T			Likely benign (Oct 23, 2022)
4-88521773-G-C			Likely benign (Dec 01, 2023)
4-88521774-G-A			Uncertain significance (May 29, 2022)
4-88521789-T-C			Uncertain significance (Jun 28, 2022)
4-88521942-C-CTG		Mitochondrial disease	Pathogenic (Jan 18, 2021)
4-88522011-G-A			Benign (Sep 05, 2018)
4-88523588-T-G		not specified	Uncertain significance (Sep 01, 2021)
4-88523591-G-A		Hyperphosphatasia with intellectual disability syndrome 6	Uncertain significance (Dec 01, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PYURF	protein_coding	protein_coding	ENST00000273968	2	2829

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.162	0.652	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.387	55	63.7	0.864	0.00000322	713
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
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

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pyurf

Gene ontology

• Biological process: GPI anchor biosynthetic process;positive regulation of metabolic process
• Cellular component: glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex;mitochondrion;endoplasmic reticulum membrane;cytosol
• Molecular function: protein binding