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.

• 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.

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				6	2	8
missense		2	28	4		34
nonsense		3				3
start loss						0
frameshift	1	2				3
inframe indel						0
splice donor/acceptor (+/-2bp)					1	1
splice region						0
non coding					3	3
Total	1	7	28	10	6

Variants in MINPP1

This is a list of pathogenic ClinVar variants found in the MINPP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-87504931-G-C		not specified	Likely benign (Apr 06, 2024)
10-87504950-C-T		not specified	Uncertain significance (May 26, 2022)
10-87504966-G-A			Likely benign (Jun 15, 2018)
10-87504971-T-C		Pontocerebellar hypoplasia, type 16	Uncertain significance (Mar 25, 2024)
10-87504978-GGCGCTGCTCTCGTCGCTTGC-G		Pontocerebellar hypoplasia, type 16	Likely pathogenic (Mar 29, 2021)
10-87505014-A-G			Likely benign (Nov 27, 2017)
10-87505029-G-T			Likely benign (May 01, 2024)
10-87505037-C-T		Thyroid cancer, nonmedullary, 2	Pathogenic (Apr 01, 2001)
10-87505072-T-G		Pontocerebellar hypoplasia, type 16	Likely pathogenic (Mar 28, 2022)
10-87505086-C-T		MINPP1-related disorder	Likely benign (May 01, 2022)
10-87505090-G-A		not specified	Uncertain significance (Oct 06, 2021)
10-87505090-G-T		not specified	Uncertain significance (Feb 16, 2023)
10-87505123-G-A		not specified	Uncertain significance (May 16, 2024)
10-87505136-T-TGGGGG		Pontocerebellar hypoplasia, type 16	Pathogenic (Sep 08, 2022)
10-87505138-G-C			Likely benign (Nov 10, 2017)
10-87505147-T-C		not specified	Uncertain significance (May 18, 2023)
10-87505152-C-A			Likely benign (Jun 17, 2018)
10-87505214-GC-G		Pontocerebellar hypoplasia, type 16	Pathogenic (Sep 08, 2022)
10-87505255-T-C		not specified	Likely benign (Jan 04, 2022)
10-87505267-G-A		not specified	Likely benign (Oct 29, 2021)
10-87505306-C-A		not specified	Uncertain significance (May 17, 2023)
10-87505338-G-C		not specified	Uncertain significance (Jan 23, 2024)
10-87505366-C-T		not specified	Uncertain significance (Dec 28, 2022)
10-87505411-C-T		not specified	Uncertain significance (Oct 21, 2024)
10-87505426-C-G		not specified	Uncertain significance (Aug 12, 2024)

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-<i>myo</i>-inositol (1,3,4)-trisphosphate biosynthesis;superpathway of D-<i>myo</i>-inositol (1,4,5)-trisphosphate metabolism;Metabolism;Rapoport-Luebering glycolytic shunt;superpathway of inositol phosphate compounds;Phosphatidylinositol phosphate metabolism;D-<i>myo</i>-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