PHOSPHO2

phosphatase, orphan 2, the group of HAD Asp-based non-protein phosphatases

Basic information

Region (hg38): 2:169694454-169701708

Links

ENSG00000144362 ∙ NCBI:493911 ∙ ∙ HGNC:28316 ∙ Uniprot:Q8TCD6 ∙ 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 PHOSPHO2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PHOSPHO2 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						0
missense			11	1		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	1	0

Variants in PHOSPHO2

This is a list of pathogenic ClinVar variants found in the PHOSPHO2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-169700976-A-G		not specified	Uncertain significance (Dec 14, 2021)
2-169701008-A-G		not specified	Uncertain significance (Apr 04, 2023)
2-169701021-A-G		not specified	Uncertain significance (Mar 24, 2023)
2-169701195-C-A		not specified	Uncertain significance (Aug 10, 2021)
2-169701203-A-G		not specified	Uncertain significance (Mar 06, 2023)
2-169701255-T-C		not specified	Uncertain significance (Dec 03, 2024)
2-169701266-G-T		not specified	Uncertain significance (Jan 26, 2023)
2-169701276-C-T		not specified	Uncertain significance (Apr 22, 2022)
2-169701284-A-T		not specified	Uncertain significance (Dec 07, 2024)
2-169701309-G-A		not specified	Likely benign (Nov 15, 2021)
2-169701461-C-G		not specified	Uncertain significance (Jun 27, 2022)
2-169701501-T-C		not specified	Uncertain significance (Jun 06, 2023)
2-169701576-A-T		not specified	Uncertain significance (Sep 27, 2024)
2-169701609-A-C		not specified	Uncertain significance (Aug 21, 2024)
2-169701615-T-A		not specified	Uncertain significance (Jul 16, 2024)
2-169701682-T-G		not specified	Uncertain significance (Nov 17, 2022)
2-169701686-A-G		not specified	Uncertain significance (Mar 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PHOSPHO2	protein_coding	protein_coding	ENST00000359744	1	7244

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000200	0.501	125674	0	31	125705	0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.714	102	124	0.820	0.00000578	1612
Missense in Polyphen		33	47.047	0.70142		614
Synonymous	1.19	31	40.6	0.763	0.00000183	437
Loss of Function	0.377	6	7.08	0.847	3.62e-7	94

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000179	0.000177
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000231	0.000231
European (Non-Finnish)	0.000106	0.000106
Middle Eastern	0.000109	0.000109
South Asian	0.000196	0.000196
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Phosphatase that has high activity toward pyridoxal 5'- phosphate (PLP). Also active at much lower level toward pyrophosphate, phosphoethanolamine (PEA), phosphocholine (PCho), phospho-l-tyrosine, fructose-6-phosphate, p-nitrophenyl phosphate, and h-glycerophosphate.
• Pathway: Vitamin B6 metabolism - Homo sapiens (human);pyridoxal 5,-phosphate salvage (Consensus)

Intolerance Scores

• loftool: 0.793
• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.19

Haploinsufficiency Scores

• pHI: 0.0897
• hipred: N
• hipred_score: 0.292
• ghis: 0.506

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.138

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Phospho2

Gene ontology

• Biological process: dephosphorylation
• Molecular function: protein binding;pyridoxal phosphatase activity;metal ion binding