PHOSPHO1

phosphoethanolamine/phosphocholine phosphatase 1, the group of HAD Asp-based non-protein phosphatases

Basic information

Region (hg38): 17:49223366-49230787

Links

ENSG00000173868

∙ NCBI:162466 ∙ ∙ HGNC:16815 ∙ Uniprot:Q8TCT1 ∙ 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 PHOSPHO1 gene.

not_specified (35 variants)
not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PHOSPHO1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000178500.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			27 clinvar			27
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	27	1	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PHOSPHO1	protein_coding	protein_coding	ENST00000413580	1	7405

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.514	0.470	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.17	122	164	0.742	0.00000748	1841
Missense in Polyphen		49	69.376	0.70629		781
Synonymous	1.49	58	74.4	0.780	0.00000354	603
Loss of Function	1.94	1	6.20	0.161	2.67e-7	65

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

Function: FUNCTION: Phosphatase that has a high activity toward phosphoethanolamine (PEA) and phosphocholine (PCho). Involved in the generation of inorganic phosphate for bone mineralization.;
Pathway: Glycerophospholipid metabolism - Homo sapiens (human);Phospholipid Biosynthesis;Metabolism of lipids;Metabolism;Synthesis of PC;Synthesis of PE;Glycerophospholipid biosynthesis;Phospholipid metabolism (Consensus)

Recessive Scores

pRec: 0.115

Haploinsufficiency Scores

pHI: 0.254
hipred: Y
hipred_score: 0.507
ghis: 0.405

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.947

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Phospho1
Phenotype: growth/size/body region phenotype; homeostasis/metabolism phenotype; limbs/digits/tail phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype;

Gene ontology

Biological process: endochondral ossification;phosphatidylethanolamine biosynthetic process;phosphatidylcholine biosynthetic process;dephosphorylation;regulation of bone mineralization;bone mineralization involved in bone maturation
Cellular component: cytosol;extracellular matrix;extracellular membrane-bounded organelle
Molecular function: pyrophosphatase activity;metal ion binding;phosphocholine phosphatase activity;phosphoethanolamine phosphatase activity