PHPT1

phosphohistidine phosphatase 1, the group of Protein phosphatases

Basic information

Region (hg38): 9:136848724-136851027

Links

ENSG00000054148 ∙ NCBI:29085 ∙ OMIM:610167 ∙ HGNC:30033 ∙ Uniprot:Q9NRX4 ∙ 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 PHPT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PHPT1 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			17	2	1	20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	3	1

Variants in PHPT1

This is a list of pathogenic ClinVar variants found in the PHPT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-136849435-C-T		not specified	Uncertain significance (Jan 10, 2025)
9-136849438-T-C			Benign (Apr 04, 2018)
9-136849443-G-A		not specified	Uncertain significance (Nov 13, 2024)
9-136849465-T-C		not specified	Uncertain significance (Feb 27, 2023)
9-136849490-C-G		not specified	Uncertain significance (Feb 02, 2022)
9-136849505-C-G		not specified	Uncertain significance (Apr 08, 2024)
9-136849537-C-T		not specified	Uncertain significance (Jan 10, 2025)
9-136849547-G-C			Likely benign (Aug 01, 2023)
9-136849564-G-A		not specified	Uncertain significance (Oct 12, 2022)
9-136850024-G-C		not specified	Uncertain significance (May 28, 2024)
9-136850047-G-A			Likely benign (Mar 01, 2022)
9-136850071-T-G		not specified	Uncertain significance (May 28, 2024)
9-136850081-G-A		not specified	Uncertain significance (Oct 10, 2023)
9-136850089-C-G		not specified	Uncertain significance (Oct 07, 2024)
9-136850095-C-A		not specified	Uncertain significance (Dec 13, 2024)
9-136850103-A-G		not specified	Uncertain significance (Dec 13, 2022)
9-136850112-A-T		not specified	Uncertain significance (Feb 22, 2025)
9-136850132-T-A		not specified	Uncertain significance (Mar 28, 2022)
9-136850133-C-A		not specified	Uncertain significance (Mar 28, 2022)
9-136850759-A-G		not specified	Uncertain significance (Dec 21, 2022)
9-136850765-C-T		not specified	Uncertain significance (Feb 27, 2025)
9-136850775-C-T		not specified	Likely benign (Feb 27, 2025)
9-136850776-G-T		not specified	Likely benign (May 09, 2023)
9-136850782-T-G		not specified	Uncertain significance (Feb 05, 2024)
9-136850785-A-G		not specified	Uncertain significance (Mar 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PHPT1	protein_coding	protein_coding	ENST00000247665	3	2313

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000643	0.296	125469	0	71	125540	0.000283

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.352	91	82.0	1.11	0.00000451	812
Missense in Polyphen		36	35.884	1.0032		336
Synonymous	-2.49	56	36.8	1.52	0.00000259	235
Loss of Function	-0.216	6	5.46	1.10	2.36e-7	59

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000356	0.000356
Ashkenazi Jewish	0.000998	0.000994
East Asian	0.000218	0.000218
Finnish	0.000508	0.000508
European (Non-Finnish)	0.000221	0.000220
Middle Eastern	0.000218	0.000218
South Asian	0.000329	0.000327
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Exhibits phosphohistidine phosphatase activity. {ECO:0000269|PubMed:19836471, ECO:0000269|PubMed:25574816}.
• Pathway: Fructose intolerance, hereditary;Fructose and Mannose Degradation;Fructosuria;EGFR1 (Consensus)

Intolerance Scores

• loftool: 0.341
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.2

Haploinsufficiency Scores

• pHI: 0.102
• hipred: N
• hipred_score: 0.170
• ghis: 0.583

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.813

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Phpt1
• Phenotype: skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: protein dephosphorylation;positive regulation of insulin secretion involved in cellular response to glucose stimulus;peptidyl-histidine dephosphorylation;negative regulation of T cell receptor signaling pathway;negative regulation of lyase activity;positive regulation of cell motility;regulation of actin cytoskeleton reorganization;negative regulation of ATP citrate synthase activity
• Cellular component: cytosol;extracellular exosome
• Molecular function: protein binding;calcium channel inhibitor activity;ion channel binding;protein histidine phosphatase activity