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.

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.

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			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	1	0

Variants in PHOSPHO1

This is a list of pathogenic ClinVar variants found in the PHOSPHO1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-49224342-C-A		not specified	Uncertain significance (Jan 31, 2023)
17-49224362-G-A		not specified	Uncertain significance (Sep 17, 2021)
17-49224362-G-T		not specified	Uncertain significance (Aug 23, 2021)
17-49224401-C-A		not specified	Uncertain significance (Mar 06, 2023)
17-49224406-G-A		not specified	Uncertain significance (Dec 20, 2023)
17-49224460-C-A		not specified	Uncertain significance (May 03, 2023)
17-49224460-C-T		not specified	Uncertain significance (Mar 24, 2023)
17-49224493-C-T		not specified	Uncertain significance (Dec 27, 2023)
17-49224550-C-G		not specified	Uncertain significance (Apr 07, 2023)
17-49224568-C-A		not specified	Uncertain significance (Oct 05, 2022)
17-49224648-G-A			Likely benign (Mar 01, 2022)
17-49224683-C-T		not specified	Uncertain significance (Feb 13, 2024)
17-49224739-T-G		not specified	Uncertain significance (Mar 01, 2023)
17-49224932-C-G		not specified	Uncertain significance (May 05, 2023)
17-49224964-A-G		not specified	Uncertain significance (Sep 14, 2022)
17-49224973-C-G		not specified	Uncertain significance (Jan 19, 2024)
17-49225001-C-G		not specified	Uncertain significance (Mar 15, 2024)
17-49225001-C-T		not specified	Uncertain significance (Oct 17, 2023)
17-49225004-C-T		not specified	Uncertain significance (May 22, 2024)
17-49225022-A-G		not specified	Uncertain significance (Apr 12, 2022)
17-49225115-G-C		not specified	Uncertain significance (Jun 17, 2024)
17-49225117-T-C		not specified	Uncertain significance (Nov 21, 2023)

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