INPP4A

inositol polyphosphate-4-phosphatase type I A, the group of C2 domain containing

Basic information

Region (hg38): 2:98444853-98594392

Previous symbols: [ "INPP4" ]

Links

ENSG00000040933 ∙ NCBI:3631 ∙ OMIM:600916 ∙ HGNC:6074 ∙ Uniprot:Q96PE3 ∙ 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 INPP4A gene.

• Inborn genetic diseases (25 variants)
• not provided (12 variants)
• Pectus excavatum;Nystagmus;Microcephaly;Hypotonia;visual disturbance (1 variants)
• Dyskeratosis congenita, autosomal dominant 1 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the INPP4A 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	7	10
missense			25	1		26
nonsense						0
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				1		1
Total	0	2	25	4	7

Variants in INPP4A

This is a list of pathogenic ClinVar variants found in the INPP4A region.

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

Position	Type	Phenotype	Significance	ClinVar
2-98520084-C-T		Dyskeratosis congenita, autosomal dominant 1	Likely pathogenic (Oct 09, 2017)
2-98520092-G-A		not specified	Uncertain significance (Dec 01, 2022)
2-98520694-A-G		not specified	Uncertain significance (Jan 04, 2022)
2-98520695-C-T		Intellectual disability	Pathogenic (Dec 01, 2019)
2-98533407-A-G		not specified	Uncertain significance (Jun 29, 2023)
2-98533471-G-A			Likely benign (Oct 23, 2018)
2-98535782-T-A			Likely benign (Sep 24, 2018)
2-98535806-ACT-A		Pectus excavatum;Nystagmus;Microcephaly;Hypotonia;visual disturbance	Likely pathogenic (Jun 20, 2019)
2-98535813-G-A		not specified	Uncertain significance (Sep 07, 2022)
2-98535834-T-G		not specified	Uncertain significance (Feb 26, 2024)
2-98538979-C-T		not specified	Uncertain significance (Oct 12, 2021)
2-98539530-T-C		not specified	Uncertain significance (Nov 17, 2022)
2-98539535-T-C			Benign (Dec 31, 2019)
2-98539536-G-A		not specified	Uncertain significance (May 06, 2022)
2-98539636-G-A		not specified	Uncertain significance (Jul 25, 2023)
2-98543878-G-A		not specified	Uncertain significance (May 25, 2022)
2-98543909-C-A		not specified	Uncertain significance (Sep 14, 2022)
2-98543945-C-T		not specified	Uncertain significance (Aug 14, 2023)
2-98543988-C-T			Benign (Dec 31, 2019)
2-98543999-A-G		not specified	Uncertain significance (Jan 02, 2024)
2-98546603-G-A		not specified	Uncertain significance (Feb 16, 2023)
2-98552949-C-T		not specified	Uncertain significance (Oct 04, 2022)
2-98554278-A-G		not specified	Uncertain significance (Dec 16, 2022)
2-98554352-A-G		not specified	Uncertain significance (Apr 04, 2023)
2-98554381-T-C			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
INPP4A	protein_coding	protein_coding	ENST00000074304	24	149537

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000485	124658	0	9	124667	0.0000361

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.35	357	585	0.611	0.0000368	6344
Missense in Polyphen		128	267.58	0.47836		2835
Synonymous	0.691	224	238	0.943	0.0000162	1886
Loss of Function	5.84	7	52.8	0.133	0.00000279	597

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000170	0.000162
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.0000273	0.0000265
Middle Eastern	0.00	0.00
South Asian	0.0000333	0.0000327
Other	0.000178	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the hydrolysis of the 4-position phosphate of phosphatidylinositol 3,4-bisphosphate, inositol 1,3,4- trisphosphate and inositol 3,4-bisphosphate.
• Pathway: Inositol phosphate metabolism - Homo sapiens (human);Phosphatidylinositol signaling system - Homo sapiens (human);Inositol Phosphate Metabolism;Inositol Metabolism;Insulin Signaling;Metabolism of lipids;Inositol phosphate metabolism;3-phosphoinositide degradation;Metabolism;Inositol phosphate metabolism;Synthesis of PIPs at the early endosome membrane;Synthesis of PIPs at the plasma membrane;PI Metabolism;Phospholipid metabolism;Synthesis of IP2, IP, and Ins in the cytosol (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.270
• rvis_EVS: -1.24
• rvis_percentile_EVS: 5.46

Haploinsufficiency Scores

• pHI: 0.271
• hipred: Y
• hipred_score: 0.724
• ghis: 0.620

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.877

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Inpp4a
• Phenotype: muscle phenotype; growth/size/body region 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); 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: phosphatidylinositol biosynthetic process;signal transduction;dephosphorylation;phosphatidylinositol-3-phosphate biosynthetic process;inositol phosphate metabolic process
• Cellular component: cytoplasm;cytosol
• Molecular function: protein binding;phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity;inositol-1,3,4-trisphosphate 4-phosphatase activity;phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity;inositol-3,4-bisphosphate 4-phosphatase activity