INPP4A

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

Basic information

Region (hg38): 2:98444854-98594392

Previous symbols: [ "INPP4" ]

Links

ENSG00000040933 ∙ NCBI:3631 ∙ OMIM:600916 ∙ HGNC:6074 ∙ Uniprot:Q96PE3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 79.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_001134225.2	NP_001127697.1	23	yes	-
ENST00000409851.8	ENSP00000386777.4	23	yes	-
NM_001566.2	NP_001557.1	24	-	-
NM_004027.3	NP_004018.1	24	-	-

Phenotypes

GenCC

Source: genCC

• neurodevelopmental disorder (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the INPP4A gene.

• not_specified (89 variants)
• not_provided (17 variants)
• Neurodevelopmental_disorder_with_growth_impairment,_quadriparesis,_and_poor_or_absent_speech (6 variants)
• Hypotonia (1 variants)
• Pectus_excavatum (1 variants)
• Nystagmus (1 variants)
• Dyskeratosis_congenita,_autosomal_dominant_1 (1 variants)
• visual_disturbance (1 variants)
• Microcephaly (1 variants)
• Intellectual_disability (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. These statistics are base on transcript: NM_001134225.2. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous		1	2	5	6	14
missense	1		98	2		101
nonsense	2		4			6
start loss						0
frameshift	1	1				2
splice donor/acceptor (+/-2bp)	3		4			7
Total	7	2	108	7	6

Highest pathogenic variant AF is 0.0000014888219

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
		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

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

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