IMPA2

inositol monophosphatase 2, the group of Phosphoinositide phosphatases

Basic information

Region (hg38): 18:11981024-12030877

Links

ENSG00000141401 ∙ NCBI:3613 ∙ OMIM:605922 ∙ HGNC:6051 ∙ Uniprot:O14732 ∙ 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 IMPA2 gene.

• Inborn genetic diseases (18 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IMPA2 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			18		1	19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding						0
Total	0	0	18	0	1

Variants in IMPA2

This is a list of pathogenic ClinVar variants found in the IMPA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-11981677-C-T		not specified	Uncertain significance (Apr 12, 2023)
18-11981698-C-T		not specified	Uncertain significance (Jan 29, 2024)
18-11981734-C-A		not specified	Uncertain significance (Jul 13, 2021)
18-11981742-C-G		not specified	Uncertain significance (Nov 16, 2021)
18-11981745-C-G		not specified	Uncertain significance (Nov 16, 2021)
18-11981749-C-G		not specified	Uncertain significance (Nov 16, 2021)
18-11981751-C-G		not specified	Uncertain significance (Nov 16, 2021)
18-11981752-T-G		not specified	Uncertain significance (Nov 16, 2021)
18-11981754-C-G		not specified	Uncertain significance (Jul 08, 2021)
18-12009876-A-G			Benign (Jun 26, 2018)
18-12009902-G-A		not specified	Uncertain significance (Jun 06, 2023)
18-12009903-C-T		not specified	Uncertain significance (Apr 09, 2022)
18-12009914-G-A			Benign (Aug 24, 2018)
18-12009918-A-G		not specified	Uncertain significance (Aug 02, 2021)
18-12012192-A-G		not specified	Uncertain significance (Aug 17, 2022)
18-12014311-C-T		not specified	Uncertain significance (Nov 30, 2022)
18-12014317-G-A		not specified	Uncertain significance (Jun 22, 2021)
18-12028043-A-G		not specified	Uncertain significance (Nov 08, 2022)
18-12028045-C-G		not specified	Uncertain significance (Jun 05, 2023)
18-12028084-C-T		not specified	Uncertain significance (Jul 11, 2023)
18-12028940-C-T		not specified	Uncertain significance (Jun 29, 2023)
18-12028978-G-A		not specified	Uncertain significance (Oct 16, 2023)
18-12028988-C-A		not specified	Uncertain significance (Feb 28, 2024)
18-12030339-C-G			Benign (Jun 17, 2018)
18-12030441-C-T		not specified	Uncertain significance (Sep 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IMPA2	protein_coding	protein_coding	ENST00000269159	8	49853

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00106	0.955	125730	0	18	125748	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.851	140	171	0.817	0.0000114	1827
Missense in Polyphen		52	75.585	0.68797		780
Synonymous	0.695	64	71.5	0.895	0.00000499	614
Loss of Function	1.77	7	14.2	0.492	8.38e-7	170

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000216	0.000216
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.0000705	0.0000703
Middle Eastern	0.000218	0.000217
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Can use myo-inositol monophosphates, scylloinositol 1,4- diphosphate, glucose-1-phosphate, beta-glycerophosphate, and 2'- AMP as substrates. Has been implicated as the pharmacological target for lithium Li(+) action in brain. {ECO:0000269|PubMed:17068342}.
• Pathway: Inositol phosphate metabolism - Homo sapiens (human);Phosphatidylinositol signaling system - Homo sapiens (human);superpathway of D-<i>myo</i>-inositol (1,4,5)-trisphosphate metabolism;Inositol phosphate metabolism;D-<i>myo</i>-inositol (1,4,5)-trisphosphate degradation;Metabolism;<i>myo</i>-inositol <i>de novo</i> biosynthesis;Inositol phosphate metabolism;Synthesis of IP2, IP, and Ins in the cytosol (Consensus)

Recessive Scores

• pRec: 0.236

Intolerance Scores

• loftool: 0.424
• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.27

Haploinsufficiency Scores

• pHI: 0.539
• hipred: Y
• hipred_score: 0.654
• ghis: 0.417

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.898

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Impa2
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); renal/urinary system phenotype; normal phenotype

Gene ontology

• Biological process: inositol biosynthetic process;phosphate-containing compound metabolic process;signal transduction;inositol phosphate metabolic process;phosphatidylinositol phosphorylation;inositol phosphate dephosphorylation
• Cellular component: cytoplasm;cytosol
• Molecular function: protein binding;inositol monophosphate 1-phosphatase activity;protein homodimerization activity;metal ion binding;inositol monophosphate 3-phosphatase activity;inositol monophosphate 4-phosphatase activity