Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	8398
Gene name Gene Name - the full gene name approved by the HGNC.	Phospholipase A2 group VI
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	PLA2G6
Synonyms (NCBI Gene) Gene synonyms aliases	CaI-PLA2, GVI, INAD1, IPLA2-VIA, NBIA2, NBIA2A, NBIA2B, PARK14, PLA2, PNPLA9, iPLA2, iPLA2beta
Chromosome Chromosome number	22
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	22q13.1
Summary Summary of gene provided in NCBI Entrez Gene.	The protein encoded by this gene is an A2 phospholipase, a class of enzyme that catalyzes the release of fatty acids from phospholipids. The encoded protein may play a role in phospholipid remodelling, arachidonic acid release, leukotriene and prostagland

Show/Hide all(80)

SNP ID	Visualize variation	Clinical significance	Consequence
rs121908681	T>C,G	Pathogenic, likely-pathogenic	Coding sequence variant, missense variant
rs121908682	A>T	Pathogenic	Coding sequence variant, missense variant
rs121908683	G>A	Pathogenic	Coding sequence variant, missense variant
rs121908685	C>A,T	Uncertain-significance, pathogenic	Coding sequence variant, 5 prime UTR variant, missense variant
rs141045127	C>T	Likely-pathogenic	Coding sequence variant, missense variant
rs141825182	C>T	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Coding sequence variant, 5 prime UTR variant, missense variant
rs147455037	C>T	Uncertain-significance, likely-pathogenic	Coding sequence variant, missense variant
rs149712244	C>T	Pathogenic, likely-pathogenic	Coding sequence variant, missense variant
rs199935023	C>A,T	Uncertain-significance, conflicting-interpretations-of-pathogenicity, pathogenic	Coding sequence variant, missense variant
rs200075782	G>A,C	Pathogenic	Coding sequence variant, 5 prime UTR variant, stop gained, missense variant
rs368497893	C>T	Pathogenic	Coding sequence variant, synonymous variant
rs370288820	G>A	Conflicting-interpretations-of-pathogenicity	Intron variant
rs370691849	G>A,T	Pathogenic, likely-pathogenic	Missense variant, coding sequence variant
rs374746113	A>G	Likely-pathogenic, uncertain-significance	Missense variant, 5 prime UTR variant, coding sequence variant
rs387906863	C>A,T	Pathogenic, uncertain-significance	Missense variant, coding sequence variant
rs387906864	G>A,C	Pathogenic	Stop gained, missense variant, coding sequence variant
rs528966598	C>T	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs535486098	C>T	Pathogenic, likely-pathogenic	Missense variant, coding sequence variant
rs547175863	G>C	Likely-pathogenic	Missense variant, coding sequence variant
rs587784326	G>A	Likely-pathogenic	Coding sequence variant, missense variant
rs587784327	C>T	Pathogenic, likely-pathogenic	Coding sequence variant, missense variant
rs587784329	G>-	Pathogenic, likely-pathogenic	Frameshift variant, coding sequence variant
rs587784330	A>T	Pathogenic	Coding sequence variant, missense variant
rs587784331	G>A	Likely-pathogenic	Coding sequence variant, missense variant
rs587784332	C>G,T	Uncertain-significance, pathogenic	Coding sequence variant, missense variant
rs587784333	G>-	Pathogenic	Frameshift variant, coding sequence variant
rs587784336	C>-	Pathogenic	Frameshift variant, coding sequence variant
rs587784337	C>T	Pathogenic	Coding sequence variant, missense variant
rs587784338	G>A	Pathogenic	Coding sequence variant, missense variant
rs587784339	G>A	Pathogenic	Coding sequence variant, stop gained
rs587784340	T>C,G	Likely-pathogenic	Coding sequence variant, missense variant
rs587784341	G>A	Likely-pathogenic	Coding sequence variant, missense variant
rs587784343	AAC>-	Pathogenic	Inframe deletion, coding sequence variant
rs587784346	G>A	Pathogenic	Coding sequence variant, stop gained
rs587784347	G>A	Likely-pathogenic	Coding sequence variant, missense variant
rs587784355	A>G	Likely-pathogenic	Missense variant, coding sequence variant, 5 prime UTR variant
rs587784356	G>T	Likely-pathogenic	Missense variant, coding sequence variant, 5 prime UTR variant
rs587784357	G>A	Pathogenic	Synonymous variant, coding sequence variant, 5 prime UTR variant, stop gained
rs587784359	G>A	Pathogenic, likely-pathogenic	Intron variant, coding sequence variant, missense variant
rs587784360	CGAGCATTGCAC>-	Likely-pathogenic	Inframe deletion, intron variant, coding sequence variant
rs587784361	T>-	Pathogenic	Intron variant, frameshift variant, coding sequence variant
rs587784362	A>C,G	Pathogenic	Coding sequence variant, missense variant
rs587784363	C>A,T	Pathogenic, likely-pathogenic	Coding sequence variant, missense variant
rs587784364	A>G	Likely-pathogenic	Coding sequence variant, missense variant
rs730882214	G>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs745643715	C>T	Likely-pathogenic	Intron variant, coding sequence variant, missense variant
rs750939090	C>T	Likely-pathogenic, pathogenic-likely-pathogenic	Splice donor variant
rs761815070	C>A,T	Likely-pathogenic	Splice donor variant
rs764959600	C>A,T	Pathogenic	Missense variant, initiator codon variant, 5 prime UTR variant
rs774631197	G>A,T	Pathogenic	Synonymous variant, missense variant, coding sequence variant, 5 prime UTR variant
rs776713955	C>T	Pathogenic	Missense variant, coding sequence variant
rs794729212	C>T	Likely-pathogenic	Missense variant, coding sequence variant
rs797044903	TTGGCCC>-	Pathogenic	Frameshift variant, coding sequence variant
rs797045888	T>C	Pathogenic	Splice acceptor variant
rs797045889	->CGG	Likely-pathogenic	Coding sequence variant, inframe insertion
rs886039552	G>A	Pathogenic	Coding sequence variant, 5 prime UTR variant, stop gained
rs1025497590	C>G,T	Pathogenic	Splice acceptor variant
rs1057521104	A>G	Likely-pathogenic	5 prime UTR variant, coding sequence variant, missense variant
rs1060499764	T>C	Likely-pathogenic	Coding sequence variant, missense variant
rs1064795344	T>G	Likely-pathogenic	5 prime UTR variant, coding sequence variant, missense variant
rs1064796469	C>G	Likely-pathogenic	Intron variant
rs1175689296	T>C	Conflicting-interpretations-of-pathogenicity	Intron variant
rs1177564212	C>G,T	Pathogenic	Missense variant, coding sequence variant, 5 prime UTR variant, stop gained
rs1282370486	A>-	Pathogenic	Coding sequence variant, intron variant, frameshift variant
rs1356679312	A>G	Likely-pathogenic	Coding sequence variant, missense variant
rs1416924105	G>A	Likely-pathogenic	Stop gained, 5 prime UTR variant, coding sequence variant
rs1451486649	G>A,C,T	Likely-pathogenic	Coding sequence variant, missense variant
rs1465629909	T>G	Pathogenic	Splice acceptor variant
rs1477656610	C>T	Pathogenic	Intron variant, splice acceptor variant
rs1555978219	T>C	Likely-pathogenic	Missense variant, coding sequence variant
rs1555979401	C>G	Likely-pathogenic	Splice acceptor variant
rs1555988204	->GC	Pathogenic	Coding sequence variant, frameshift variant
rs1555988382	C>G	Likely-pathogenic	Missense variant, coding sequence variant
rs1556010444	C>G	Pathogenic	Missense variant, coding sequence variant
rs1556032708	G>A	Likely-pathogenic	5 prime UTR variant, coding sequence variant, stop gained
rs1569243565	A>-	Pathogenic	Coding sequence variant, frameshift variant
rs1569243771	G>-	Pathogenic	Intron variant
rs1569264087	A>G	Likely-pathogenic	Missense variant, coding sequence variant
rs1602057157	T>C	Pathogenic	Splice acceptor variant
rs1602088419	A>C	Likely-pathogenic	Missense variant, coding sequence variant

Show/Hide all(9)

miRTarBase ID	miRNA	Experiments
MIRT1238850	hsa-miR-1275	CLIP-seq
MIRT1238851	hsa-miR-3160-3p	CLIP-seq
MIRT1238852	hsa-miR-409-3p	CLIP-seq
MIRT1238853	hsa-miR-4487	CLIP-seq
MIRT1238854	hsa-miR-4525	CLIP-seq
MIRT1238855	hsa-miR-4665-5p	CLIP-seq
MIRT1238856	hsa-miR-4723-5p	CLIP-seq
MIRT1238857	hsa-miR-558	CLIP-seq
MIRT1238858	hsa-miR-625	CLIP-seq

Show/Hide all(45)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003847	Function	1-alkyl-2-acetylglycerophosphocholine esterase activity	ISS
GO:0004622	Function	Phosphatidylcholine lysophospholipase activity	IDA	20886109
GO:0004622	Function	Phosphatidylcholine lysophospholipase activity	IEA
GO:0004623	Function	Phospholipase A2 activity	IEA
GO:0004623	Function	Phospholipase A2 activity	TAS	9417066
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005516	Function	Calmodulin binding	IEA
GO:0005615	Component	Extracellular space	IDA	18714013
GO:0005737	Component	Cytoplasm	IEA
GO:0005739	Component	Mitochondrion	IBA
GO:0005739	Component	Mitochondrion	IDA	38322995
GO:0005739	Component	Mitochondrion	IEA
GO:0005829	Component	Cytosol	TAS
GO:0005886	Component	Plasma membrane	IDA
GO:0005886	Component	Plasma membrane	IEA
GO:0006629	Process	Lipid metabolic process	IEA
GO:0006935	Process	Chemotaxis	IEA
GO:0015630	Component	Microtubule cytoskeleton	IDA
GO:0016020	Component	Membrane	IEA
GO:0016607	Component	Nuclear speck	IDA
GO:0016787	Function	Hydrolase activity	IEA
GO:0016787	Function	Hydrolase activity	TAS
GO:0017171	Function	Serine hydrolase activity	IEA
GO:0019731	Process	Antibacterial humoral response	IDA	18714013
GO:0031143	Component	Pseudopodium	IEA
GO:0034638	Process	Phosphatidylcholine catabolic process	IDA	20886109
GO:0035774	Process	Positive regulation of insulin secretion involved in cellular response to glucose stimulus	IEA
GO:0035774	Process	Positive regulation of insulin secretion involved in cellular response to glucose stimulus	ISS
GO:0035965	Process	Cardiolipin acyl-chain remodeling	IBA
GO:0035965	Process	Cardiolipin acyl-chain remodeling	IDA	23152787
GO:0035965	Process	Cardiolipin acyl-chain remodeling	IDA	23533611
GO:0035965	Process	Cardiolipin acyl-chain remodeling	TAS	38322995
GO:0038096	Process	Fc-gamma receptor signaling pathway involved in phagocytosis	TAS
GO:0042802	Function	Identical protein binding	IPI	32296183
GO:0042995	Component	Cell projection	IEA
GO:0046338	Process	Phosphatidylethanolamine catabolic process	ISS
GO:0046469	Process	Platelet activating factor metabolic process	ISS
GO:0046473	Process	Phosphatidic acid metabolic process	ISS
GO:0047499	Function	Calcium-independent phospholipase A2 activity	IBA
GO:0047499	Function	Calcium-independent phospholipase A2 activity	IDA	15908428, 20886109, 23533611
GO:0047499	Function	Calcium-independent phospholipase A2 activity	IEA
GO:0052816	Function	Long-chain fatty acyl-CoA hydrolase activity	IBA
GO:0052816	Function	Long-chain fatty acyl-CoA hydrolase activity	IDA	20886109
GO:0052816	Function	Long-chain fatty acyl-CoA hydrolase activity	IEA
GO:2000304	Process	Positive regulation of ceramide biosynthetic process	IBA

MIM	HGNC	e!Ensembl
603604	9039	ENSG00000184381

Protein

UniProt ID

O60733

Protein name

85/88 kDa calcium-independent phospholipase A2 (CaI-PLA2) (EC 3.1.1.4) (2-lysophosphatidylcholine acylhydrolase) (EC 3.1.1.5) (Group VI phospholipase A2) (GVI PLA2) (Intracellular membrane-associated calcium-independent phospholipase A2 beta) (iPLA2-beta)

Protein function

Calcium-independent phospholipase involved in phospholipid remodeling with implications in cellular membrane homeostasis, mitochondrial integrity and signal transduction. Hydrolyzes the ester bond of the fatty acyl group attached at sn-1 or sn-2

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00023	Ank	151 → 181	Ankyrin repeat	Repeat
PF00023	Ank	219 → 250	Ankyrin repeat	Repeat
PF00023	Ank	316 → 348	Ankyrin repeat	Repeat
PF00023	Ank	349 → 381	Ankyrin repeat	Repeat
PF01734	Patatin	481 → 665	Patatin-like phospholipase	Family

Tissue specificity

TISSUE SPECIFICITY: Four different transcripts were found to be expressed in a distinct tissue distribution.

Sequence

MQFFGRLVNTFSGVTNLFSNPFRVKEVAVADYTSSDRVREEGQLILFQNTPNRTWDCVLV
NPRNSQSGFRLFQLELEADALVNFHQYSSQLLPFYESSPQVLHTEVLQHLTDLIRNHPSW
SVAHLAVELGIRECFHHSRIISCANCAENEEGCTPLHLACRKGDGEILVELVQYCHTQMD
VTDYKGETVFHYAVQGDNSQVLQLLGRNAVAGLNQVNNQGLTPLHLACQLGKQEMVRVLL
LCNARCNIMGPNGYPIHSAMKFSQKGCAEMIISMDSSQIHSKDPRYGASPLHWAKNAEMA
RMLLKRGCNVNSTSSAGNTALHVAVMRNRFDCAIVLLTHGANADARGEHGNTPLHLAMSK
DNVEMIKALIVFGAEVDTPNDFGETPTFLASKIGRLVTRKAILTLLRTVGAEYCFPPIHG
VPAEQGSAAPHHPFSLERAQPPPISLNNLELQDLMHISRARKPAFILGSMRDEKRTHDHL
LCLDGGGVKGLIIIQLLIAIEKASGVATKDLFDWVAGTSTGGILALAILHSKSMAYMRGM
YFRMKDEVFRGSRPYESGPLEEFLKREFGEHTKMTDVRKPKVMLTGTLSDRQPAELHLFR
NYDAPETVREPRFNQNVNLRPPAQPSDQLVWRAARSSGAAPTYFRPNGRFLDGGLLANNP
TLDAMTEIHEYNQDLIRKGQANKVKKLSIVVSLGTGRSPQVPVTCVDVFRPSNPWELAKT
VFGAKELGKMVVDCCTDPDGRAVDRARAWCEMVGIQYFRLNPQLGTDIMLDEVSDTVLVN
ALWETEVYIYEHREEFQKLIQLLLSP

Sequence length

806

Interactions

View interactions

	KEGG		Reactome
	Glycerophospholipid metabolism Ether lipid metabolism Arachidonic acid metabolism Linoleic acid metabolism alpha-Linolenic acid metabolism Metabolic pathways Ras signaling pathway Efferocytosis Vascular smooth muscle contraction Fc gamma R-mediated phagocytosis Inflammatory mediator regulation of TRP channels		Acyl chain remodelling of PC Acyl chain remodelling of PE Role of phospholipids in phagocytosis COPI-independent Golgi-to-ER retrograde traffic

Show/Hide Causal Diseases (4)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Nephropathy with Pretibial Epidermolysis Bullosa and Deafness	Neurodegeneration with brain iron accumulation 2B	rs121908686, rs587784330, rs587784343, rs587784350, rs1569243771, rs149712244, rs587784353, rs1555978219, rs121908685, rs121908681, rs797045888, rs200075782, rs535486098	N/A
Neuroaxonal Dystrophy	infantile neuroaxonal dystrophy	rs1235695530, rs199935023, rs1602051017, rs1465629909, rs587784352, rs1397030516, rs587784330, rs886039552, rs1569263730, rs776713955, rs587784329, rs368497893, rs121908687, rs587784350, rs121908683 View all (31 more)	N/A
neurodegeneration with brain iron accumulation	Neurodegeneration with brain iron accumulation	rs530348521, rs587784343, rs886039552, rs121908686, rs121908683, rs1569263730, rs776713955, rs730882214, rs121908681, rs1282370486	N/A
Parkinson disease	Autosomal recessive Parkinson disease 14	rs121908687, rs387906863, rs387906864, rs774631197, rs121908686, rs121908681, rs199935023	N/A

Show/Hide Unknown Diseases (7)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Asthma	Asthma	N/A	N/A	GWAS
Breast Cancer	Breast cancer	N/A	N/A	GWAS
Diabetes	Triglyceride levels in non-type 2 diabetes, Type 2 diabetes	N/A	N/A	GWAS
Melanoma	Melanoma	N/A	N/A	GWAS
Metabolic Syndrome	Metabolic syndrome	N/A	N/A	GWAS
Pelvic Organ Prolapse	Pelvic organ prolapse	N/A	N/A	GWAS
Spastic Ataxia	spastic ataxia	N/A	N/A	ClinVar

Show/Hide Text Mining Associations (83)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Alcohol Related Disorders	Associate	20669327
Alzheimer Disease	Inhibit	22832605
Anorchia	Associate	39184971
Aphasia Broca	Associate	37403138
Asthenozoospermia	Associate	26446356
Ataxia	Associate	24130795, 36233161
Basal Ganglia Diseases	Associate	24252552
Breast Neoplasms	Associate	28618256
Carcinogenesis	Associate	34517184
Carcinoma Lewis Lung	Associate	20619503
Carcinoma Non Small Cell Lung	Associate	26245297
Cerebellar Ataxia	Associate	24252552
Cerebellar Diseases	Associate	18799783, 24130795, 27146152, 36233161, 39184971
Cerebral Hemorrhage	Associate	32474671
Cerebral Infarction	Associate	38287382
Chronic Periodontitis	Associate	25654966
Cognition Disorders	Associate	20669327, 28295203, 37403138, 39184971
Crohn Disease	Associate	31277247
Cystitis Interstitial	Associate	15937147
Demyelinating Diseases	Associate	35247231
Developmental Disabilities	Associate	39300495
Diabetes Mellitus	Stimulate	20053941
Diabetes Mellitus	Associate	23074238
Diabetes Mellitus Type 1	Associate	34770770
Diabetes Mellitus Type 2	Associate	25654966
Diffuse Neurofibrillary Tangles with Calcification	Associate	18799783
Dyskinesia Drug Induced	Associate	39184971
Dystonia	Associate	20619503, 20669327, 28295203, 31489256, 35041927, 39184971
Dystonia Dopa responsive	Associate	20669327
Epidermal Nevus	Associate	25307738
Epilepsy	Associate	24252552
Epilepsy Myoclonic Benign Adult Familial Type 1	Associate	27513994
Exfoliation Syndrome	Associate	17417602
Fractures Spontaneous	Associate	24252552
Genetic Diseases Inborn	Associate	20813170, 39184971
Glaucoma	Associate	17417602
Glioma	Associate	35862252
Hearing Loss Bilateral	Associate	40263418
Hereditary Diffuse Leukoencephalopathy with Spheroids	Associate	20886109
Heredodegenerative Disorders Nervous System	Associate	20886109, 34387792, 35247231
Hypertrophy	Associate	39184971
Hypokinesia	Associate	37403138
Idiopathic Hypersomnia	Associate	24130795
Infertility Male	Associate	26446356
Inflammation	Associate	16882668, 29472584, 34770770
Insulin Resistance	Associate	39277575
Insulinoma	Associate	17685585, 23074238
Intellectual Disability	Associate	24252552
Iron Deficiencies	Associate	24361204
Karak Syndrome	Associate	16783378, 24130795
Lewy Body Disease	Associate	18799783, 20619503, 24252552, 26668131
Lung Neoplasms	Associate	18676680
Malformations of Cortical Development	Associate	36233161
Melanoma	Associate	19578365, 23291271, 23393597, 29036293, 29753029
Melanoma Cutaneous Malignant	Associate	21962134, 23291271, 29036293
Mental Disorders	Associate	24745848
Mitochondrial Diseases	Associate	29681094, 32071291
Mobility Limitation	Associate	39184971
Multiple System Atrophy	Associate	40263418
Muscle Weakness	Associate	20669327, 28821231
NBIA2B	Associate	27196560, 37139542, 40263418
Neoplasms	Associate	16882668, 26245297, 28618256
Neoplasms Adipose Tissue	Associate	29427237
Neoplastic Syndromes Hereditary	Associate	39184971
Nerve Degeneration	Associate	32071291
Neuroaxonal Dystrophies	Associate	16783378, 17033970, 18570303, 18799783, 20226704, 20619503, 20813170, 20886109, 22416811, 24130795, 24252552, 24628589, 24745848, 26668131, 27196560 View all (14 more)
Neurodegenerative Diseases	Associate	16783378, 18570303, 20619503, 23269600, 24130795, 26668131, 27196560, 27268037, 27513994, 28821231, 29472584, 31489256, 31493761, 37403138, 39184971
Neuroferritinopathy	Associate	18570303, 28821231, 31489256, 35180557
Neuroinflammatory Diseases	Associate	38287382
Nevus	Associate	19578365, 21962134, 27993549
Ovarian Neoplasms	Associate	16882668
Pallidopyramidal syndrome	Associate	20669327, 24361204
Pantothenate Kinase Associated Neurodegeneration	Associate	16783378, 18799783, 20619503, 20886109, 23269600, 28821231, 31489256, 39419454
Parkinson Disease	Associate	18799783, 20619503, 26245297, 29472584, 30232368, 30537300, 31493761, 32071291, 32457446, 34387792, 36499697, 36706537, 38215561, 39184971, 40282414
Parkinson Disease Secondary	Associate	20619503, 20669327, 27268037, 28295203, 30788857, 37139542, 37403138, 39184971
Parkinsonian Disorders	Associate	33361639, 37139542
Parkinsonism Dystonia Infantile	Associate	18570303, 20619503, 20886109, 26668131, 27196560, 27268037, 37139542, 37403138, 39184971
Prickle1 Related Progressive Myoclonic Epilepsy with Ataxia	Associate	24130795
Prion Diseases	Associate	37139542
Severe infantile axonal neuropathy	Associate	25348461
Spastic Paraplegia Hereditary	Associate	20669327, 28295203
tinea nigra	Associate	32457446
Urinary Bladder Diseases	Associate	15937147

PLA2G6 (phospholipase A2 group VI)