LHPP

phospholysine phosphohistidine inorganic pyrophosphate phosphatase, the group of HAD Asp-based non-protein phosphatases|Haloacid dehalogenase like hydrolase domain containing

Basic information

Region (hg38): 10:124461822-124617888

Links

ENSG00000107902 ∙ NCBI:64077 ∙ OMIM:617231 ∙ HGNC:30042 ∙ Uniprot:Q9H008 ∙ 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 LHPP gene.

• Inborn genetic diseases (17 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LHPP 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		1	18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	17	0	2

Variants in LHPP

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

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

Position	Type	Phenotype	Significance	ClinVar
10-124461875-G-A		not specified	Uncertain significance (Feb 27, 2024)
10-124461887-G-C		not specified	Uncertain significance (Oct 10, 2023)
10-124461974-G-C		not specified	Uncertain significance (Dec 06, 2021)
10-124461975-A-G		not specified	Uncertain significance (Nov 10, 2022)
10-124461978-C-T		not specified	Uncertain significance (Dec 20, 2021)
10-124484149-T-C		not specified	Uncertain significance (Jan 09, 2024)
10-124484153-G-A		not specified	Uncertain significance (Dec 20, 2023)
10-124484170-T-C		not specified	Uncertain significance (Oct 24, 2023)
10-124484195-G-A		not specified	Uncertain significance (Dec 15, 2023)
10-124484213-A-G		not specified	Uncertain significance (Feb 11, 2022)
10-124484227-G-C		not specified	Uncertain significance (Mar 23, 2022)
10-124484317-A-T		not specified	Uncertain significance (Dec 05, 2022)
10-124484332-C-A			Benign (May 31, 2018)
10-124488428-G-A		not specified	Uncertain significance (Jun 29, 2023)
10-124488476-T-C		not specified	Uncertain significance (Feb 06, 2024)
10-124488484-G-A		not specified	Uncertain significance (Jun 18, 2021)
10-124488520-G-A		not specified	Uncertain significance (Jul 06, 2022)
10-124488535-A-G		not specified	Uncertain significance (May 03, 2023)
10-124488568-G-A		not specified	Uncertain significance (Mar 01, 2024)
10-124496962-C-T		not specified	Uncertain significance (Dec 02, 2022)
10-124496992-C-G		not specified	Uncertain significance (Apr 22, 2022)
10-124498072-C-A		not specified	Uncertain significance (Nov 01, 2022)
10-124498078-C-T		not specified	Uncertain significance (Dec 27, 2022)
10-124517183-G-A		not specified	Likely benign (Feb 05, 2024)
10-124517198-G-A			Benign (Jul 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LHPP	protein_coding	protein_coding	ENST00000368842	7	156055

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.63e-7	0.240	125705	0	43	125748	0.000171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0226	154	155	0.995	0.00000983	1716
Missense in Polyphen		48	55.498	0.86489		630
Synonymous	0.0589	65	65.6	0.991	0.00000470	554
Loss of Function	0.291	11	12.1	0.910	5.95e-7	152

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000492	0.000492
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000143	0.000141
Middle Eastern	0.000326	0.000326
South Asian	0.0000991	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Phosphatase that hydrolyzes imidodiphosphate, 3- phosphohistidine and 6-phospholysine. Has broad substrate specificity and can also hydrolyze inorganic diphosphate, but with lower efficiency (By similarity). {ECO:0000250}.
• Pathway: Oxidative phosphorylation - Homo sapiens (human);Metabolism of nucleotides;Metabolism;Nucleobase biosynthesis;Purine ribonucleoside monophosphate biosynthesis (Consensus)

Intolerance Scores

• loftool: 0.875
• rvis_EVS: 0.11
• rvis_percentile_EVS: 61.91

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.204
• ghis: 0.434

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.865

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lhpp

Gene ontology

• Biological process: protein dephosphorylation;phosphate-containing compound metabolic process;purine ribonucleoside monophosphate biosynthetic process;dephosphorylation
• Cellular component: nucleus;cytosol;nuclear speck
• Molecular function: magnesium ion binding;inorganic diphosphatase activity;phosphatase activity;protein homodimerization activity;protein histidine phosphatase activity