INPP5A

inositol polyphosphate-5-phosphatase A, the group of Phosphoinositide phosphatases

Basic information

Region (hg38): 10:132537786-132783480

Links

ENSG00000068383 ∙ NCBI:3632 ∙ OMIM:600106 ∙ HGNC:6076 ∙ Uniprot:Q14642 ∙ 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 INPP5A 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 INPP5A 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	2	3
missense			17			17
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	1	2

Variants in INPP5A

This is a list of pathogenic ClinVar variants found in the INPP5A region.

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

Position	Type	Phenotype	Significance	ClinVar
10-132538118-C-T		not specified	Uncertain significance (Dec 22, 2023)
10-132538121-G-A		not specified	Uncertain significance (Jun 21, 2023)
10-132538125-C-T		not specified	Uncertain significance (Apr 22, 2022)
10-132538130-G-T		not specified	Uncertain significance (Aug 21, 2023)
10-132607943-G-A		not specified	Uncertain significance (Aug 08, 2022)
10-132645871-G-A		not specified	Uncertain significance (Dec 07, 2021)
10-132645908-G-C		not specified	Uncertain significance (May 03, 2023)
10-132645933-C-T			Likely benign (Apr 03, 2018)
10-132645956-A-G		not specified	Uncertain significance (Dec 16, 2022)
10-132650446-G-A		not specified	Uncertain significance (Dec 27, 2023)
10-132697858-A-G		not specified	Uncertain significance (Sep 22, 2022)
10-132726835-G-A		not specified	Uncertain significance (Nov 13, 2023)
10-132726884-G-A			Benign (Jun 10, 2018)
10-132749539-T-C		not specified	Uncertain significance (Mar 01, 2023)
10-132749566-A-G		not specified	Uncertain significance (Jul 10, 2023)
10-132749583-A-G		not specified	Uncertain significance (Aug 30, 2022)
10-132749597-G-A			Benign (Dec 31, 2019)
10-132749771-G-A		not specified	Uncertain significance (Jun 07, 2023)
10-132749801-G-C		not specified	Uncertain significance (Feb 06, 2023)
10-132765789-A-G		not specified	Uncertain significance (Sep 20, 2023)
10-132777693-C-T		not specified	Uncertain significance (Mar 29, 2023)
10-132777774-G-C		not specified	Uncertain significance (Jul 19, 2022)
10-132780867-G-A		not specified	Uncertain significance (Oct 02, 2023)
10-132781891-G-A		not specified	Uncertain significance (Mar 24, 2023)
10-132781933-G-A		not specified	Uncertain significance (Feb 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
INPP5A	protein_coding	protein_coding	ENST00000368594	15	245656

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.981	0.0188	125742	0	6	125748	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.78	176	256	0.687	0.0000166	2739
Missense in Polyphen		42	82.86	0.50688		828
Synonymous	-0.781	112	102	1.10	0.00000730	721
Loss of Function	4.38	4	29.8	0.134	0.00000160	334

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Major isoenzyme hydrolyzing the calcium-mobilizing second messenger Ins(1,4,5)P3, this is a signal-terminating reaction.
• Pathway: Inositol phosphate metabolism - Homo sapiens (human);Phosphatidylinositol signaling system - Homo sapiens (human);D-<i>myo</i>-inositol (1,3,4)-trisphosphate biosynthesis;superpathway of D-<i>myo</i>-inositol (1,4,5)-trisphosphate metabolism;1D-<i>myo</i>-inositol hexakisphosphate biosynthesis II (mammalian);Inositol phosphate metabolism;D-<i>myo</i>-inositol (1,4,5)-trisphosphate degradation;Metabolism;superpathway of inositol phosphate compounds;Inositol phosphate metabolism;Synthesis of IP2, IP, and Ins in the cytosol (Consensus)

Recessive Scores

• pRec: 0.205

Intolerance Scores

• loftool: 0.178
• rvis_EVS: -0.42
• rvis_percentile_EVS: 25.64

Haploinsufficiency Scores

• pHI: 0.115
• hipred: Y
• hipred_score: 0.761
• ghis: 0.551

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.989

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Inpp5a
• Phenotype: homeostasis/metabolism phenotype; growth/size/body region phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: inositol phosphate metabolic process;inositol phosphate dephosphorylation;phosphatidylinositol dephosphorylation;inositol phosphate-mediated signaling
• Cellular component: plasma membrane;membrane
• Molecular function: inositol-polyphosphate 5-phosphatase activity;protein binding;PH domain binding;inositol-1,4,5-trisphosphate 5-phosphatase activity;inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity