JMJD7-PLA2G4B

JMJD7-PLA2G4B readthrough

Basic information

Region (hg38): 15:41828095-41848155

Links

ENSG00000168970 ∙ NCBI:8681 ∙ ∙ HGNC:34449 ∙ ∙ ∙ 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 JMJD7-PLA2G4B gene.

• Inborn genetic diseases (10 variants)
• not provided (6 variants)
• Neurodevelopmental disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the JMJD7-PLA2G4B 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				2	1	3
missense			7		2	9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)					1	1
splice region						0
non coding			4			4
Total	0	0	11	2	4

Variants in JMJD7-PLA2G4B

This is a list of pathogenic ClinVar variants found in the JMJD7-PLA2G4B region.

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

Position	Type	Phenotype	Significance	ClinVar
15-41828120-C-A		JMJD7-related disorder	Likely benign (Feb 26, 2019)
15-41828144-A-G		JMJD7-PLA2G4B-related disorder	Benign (Dec 06, 2019)
15-41828158-G-C		not specified	Uncertain significance (Dec 18, 2023)
15-41828174-C-T			Benign (Jul 13, 2018)
15-41834741-G-T		not specified	Uncertain significance (Feb 28, 2024)
15-41834758-C-G			Benign (Jul 13, 2018)
15-41834828-G-A		JMJD7-related disorder	Benign (Jun 11, 2019)
15-41835004-G-A		not specified	Uncertain significance (Apr 07, 2022)
15-41835024-G-A		JMJD7-related disorder	Likely benign (Apr 11, 2019)
15-41835043-C-T		not specified	Uncertain significance (Oct 03, 2022)
15-41835094-G-A		JMJD7-related disorder	Likely benign (Feb 22, 2019)
15-41835195-C-T		JMJD7-PLA2G4B-related disorder	Likely benign (Feb 19, 2019)
15-41835222-G-T			Benign (Aug 08, 2017)
15-41836816-C-G		not specified	Uncertain significance (Oct 29, 2021)
15-41836857-G-A		JMJD7-related disorder	Likely benign (May 01, 2019)
15-41836883-C-G		not specified	Uncertain significance (May 24, 2024)
15-41836907-C-T		not specified	Uncertain significance (Jun 09, 2022)
15-41837109-T-A		not specified	Uncertain significance (May 30, 2024)
15-41837124-G-T		not specified	Uncertain significance (May 24, 2023)
15-41837130-C-G		not specified	Uncertain significance (Sep 28, 2022)
15-41837162-C-T		JMJD7-PLA2G4B-related disorder	Likely benign (Apr 03, 2019)
15-41840206-C-G		not specified	Uncertain significance (Feb 23, 2023)
15-41840519-C-T		PLA2G4B-related disorder	Benign (Jun 21, 2019)
15-41840527-C-T		not specified	Uncertain significance (Feb 16, 2023)
15-41840542-A-G		not specified	Uncertain significance (Apr 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
JMJD7-PLA2G4B	protein_coding	protein_coding	ENST00000382448	25	20061

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.06e-40	3.46e-7	125344	0	404	125748	0.00161

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.99	744	606	1.23	0.0000377	6479
Missense in Polyphen		242	206.03	1.1746		2291
Synonymous	-2.79	322	264	1.22	0.0000171	2069
Loss of Function	-0.453	59	55.4	1.07	0.00000246	613

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00650	0.00628
Ashkenazi Jewish	0.000306	0.000298
East Asian	0.00238	0.00234
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.00101	0.000985
Middle Eastern	0.00238	0.00234
South Asian	0.00335	0.00334
Other	0.00148	0.00147

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Calcium-dependent phospholipase A2 that selectively hydrolyzes glycerophospholipids in the sn-2 position with a preference for arachidonoyl phospholipids. Has a much weaker activity than PLA2G4A. Isoform 3 has calcium-dependent activity against palmitoyl-arachidonyl-phosphatidylethanolamine and low level lysophospholipase activity but no activity against phosphatidylcholine. Isoform 5 does have activity against phosphatidylcholine. {ECO:0000269|PubMed:10085124, ECO:0000269|PubMed:10358058, ECO:0000269|PubMed:16617059}.
• Pathway: Inflammatory mediator regulation of TRP channels - Homo sapiens (human);Platelet activation - Homo sapiens (human);Oxytocin signaling pathway - Homo sapiens (human);Fc epsilon RI signaling pathway - Homo sapiens (human);Ether lipid metabolism - Homo sapiens (human);VEGF signaling pathway - Homo sapiens (human);Glycerophospholipid metabolism - Homo sapiens (human);Choline metabolism in cancer - Homo sapiens (human);Serotonergic synapse - Homo sapiens (human);Glutamatergic synapse - Homo sapiens (human);Long-term depression - Homo sapiens (human);GnRH signaling pathway - Homo sapiens (human);Necroptosis - Homo sapiens (human);Vascular smooth muscle contraction - Homo sapiens (human);alpha-Linolenic acid metabolism - Homo sapiens (human);Arachidonic acid metabolism - Homo sapiens (human);Linoleic acid metabolism - Homo sapiens (human);Ras signaling pathway - Homo sapiens (human);MAPK signaling pathway - Homo sapiens (human);Phospholipase D signaling pathway - Homo sapiens (human);Ovarian steroidogenesis - Homo sapiens (human);Etodolac Action Pathway;Ketoprofen Action Pathway;Ibuprofen Action Pathway;Rofecoxib Action Pathway;Acetylsalicylic Acid Action Pathway;Diflunisal Action Pathway;Leukotriene C4 Synthesis Deficiency;Acetaminophen Action Pathway;Celecoxib Action Pathway;Sulindac Action Pathway;Diclofenac Action Pathway;Ketorolac Action Pathway;Naproxen Action Pathway;Etoricoxib Action Pathway;Carprofen Action Pathway;Flurbiprofen Action Pathway;Fenoprofen Action Pathway;Antrafenine Action Pathway;Antipyrine Action Pathway;Lumiracoxib Action Pathway;Magnesium salicylate Action Pathway;Alpha Linolenic Acid and Linoleic Acid Metabolism;Trisalicylate-choline Action Pathway;Nepafenac Action Pathway;Phenylbutazone Action Pathway;Lornoxicam Action Pathway;Salsalate Action Pathway;Tenoxicam Action Pathway;Tiaprofenic Acid Action Pathway;Tolmetin Action Pathway;Salicylic Acid Action Pathway;Salicylate-sodium Action Pathway;Oxaprozin Action Pathway;Valdecoxib Action Pathway;Nabumetone Action Pathway;Phospholipid Biosynthesis;Indomethacin Action Pathway;Meloxicam Action Pathway;Suprofen Action Pathway;Bromfenac Action Pathway;Mefenamic Acid Action Pathway;Arachidonic Acid Metabolism;Piroxicam Action Pathway;Ras Signaling;Acyl chain remodelling of PG;Metabolism of lipids;Metabolism;phospholipases;Acyl chain remodelling of PC;Linoleate metabolism;Glycerophospholipid metabolism;Acyl chain remodelling of PS;Glycerophospholipid biosynthesis;Phospholipid metabolism;Hydrolysis of LPC;Acyl chain remodelling of PE;Synthesis of PA;Arachidonic acid metabolism (Consensus)

Intolerance Scores

• rvis_EVS: 0.49
• rvis_percentile_EVS: 79.48

Haploinsufficiency Scores

• pHI: 0.179
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0914