MINPP1

multiple inositol-polyphosphate phosphatase 1, the group of MicroRNA protein coding host genes|Phosphoinositide phosphatases

Basic information

Region (hg38): 10:87504875-87553461

Links

ENSG00000107789

∙ NCBI:9562 ∙ OMIM:605391 ∙ HGNC:7102 ∙ Uniprot:Q9UNW1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

thyroid cancer, nonmedullary, 2 (No Known Disease Relationship), mode of inheritance: Unknown
pontocerebellar hypoplasia type 7 (Supportive), mode of inheritance: AR
pontocerebellar hypoplasia, type 16 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Pontocerebellar hypoplasia, type 16	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic	33168985; 33257696

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MINPP1 gene.

not_specified (58 variants)
Pontocerebellar_hypoplasia,_type_16 (22 variants)
not_provided (12 variants)
Thyroid_cancer,_nonmedullary,_2 (5 variants)
MINPP1-related_disorder (3 variants)
Pontoneocerebellar_hypoplasia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MINPP1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004897.5. 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				7 clinvar	2 clinvar	9
missense	2 clinvar	3 clinvar	60 clinvar	6 clinvar		71
nonsense	1 clinvar	5 clinvar	1 clinvar			7
start loss						0
frameshift	3 clinvar	4 clinvar				7
splice donor/acceptor (+/-2bp)					1 clinvar	1
Total	6	12	61	13	3

Highest pathogenic variant AF is 0.000008214508

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MINPP1	protein_coding	protein_coding	ENST00000371996	5	48586

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000455	0.993	125730	0	18	125748	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.579	240	267	0.900	0.0000125	3151
Missense in Polyphen		51	82.298	0.6197		1020
Synonymous	0.0160	112	112	0.998	0.00000543	983
Loss of Function	2.38	9	20.7	0.435	0.00000113	229

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000182	0.000181
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000829	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.0000669	0.0000653
Other	0.000330	0.000326

dbNSFP

Source: dbNSFP

Function: FUNCTION: Acts as a phosphoinositide 5- and phosphoinositide 6- phosphatase and regulates cellular levels of inositol pentakisphosphate (InsP5) and inositol hexakisphosphate (InsP6). Also acts as a 2,3-bisphosphoglycerate 3-phosphatase, by mediating the dephosphorylation of 2,3-bisphosphoglycerate (2,3-BPG) to produce phospho-D-glycerate without formation of 3- phosphoglycerate. May play a role in bone development (endochondral ossification). May play a role in the transition of chondrocytes from proliferation to hypertrophy (By similarity). {ECO:0000250|UniProtKB:F1NPQ2, ECO:0000269|PubMed:18413611}.;
Pathway: Glycolysis / Gluconeogenesis - Homo sapiens (human);Inositol phosphate metabolism - Homo sapiens (human);Inositol Phosphate Metabolism;Inositol Metabolism;D-myo-inositol (1,3,4)-trisphosphate biosynthesis;superpathway of D-myo-inositol (1,4,5)-trisphosphate metabolism;Metabolism;Rapoport-Luebering glycolytic shunt;superpathway of inositol phosphate compounds;Phosphatidylinositol phosphate metabolism;D-myo-inositol (1,4,5,6)-tetrakisphosphate biosynthesis;Synthesis of IPs in the ER lumen;Inositol phosphate metabolism (Consensus)

Recessive Scores

pRec: 0.130

Intolerance Scores

loftool: 0.414
rvis_EVS: -0.63
rvis_percentile_EVS: 17.03

Haploinsufficiency Scores

pHI: 0.926
hipred: Y
hipred_score: 0.725
ghis: 0.604

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.976

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Minpp1
Phenotype: normal phenotype;

Gene ontology

Biological process: ossification;protein dephosphorylation;polyphosphate metabolic process;bone mineralization;inositol phosphate metabolic process
Cellular component: endoplasmic reticulum;endoplasmic reticulum lumen;extracellular exosome
Molecular function: acid phosphatase activity;inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity;bisphosphoglycerate 3-phosphatase activity;inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity;inositol phosphate phosphatase activity;inositol hexakisphosphate 2-phosphatase activity;protein histidine phosphatase activity