JMJD7-PLA2G4B

protein-coding

JMJD7-PLA2G4B readthrough

Gene summary

This locus represents naturally-occurring readthrough transcription between the neighboring jumonji domain containing 7 (JMJD7) and phospholipase A2, group IVB (cytosolic) (PLA2G4B) genes. Readthrough transcripts encode fusion proteins that share amino acid sequence with each individual gene product, including a partial JmjC domain and downstream C2 and phospholipase A2 domains. Alternatively spliced transcript variants have been observed. [provided by RefSeq, Oct 2013]

MANE transcript

N/A

Inheritance

—

ClinVar variants

U:7B:6

Top phenotype

Inborn genetic diseases

gnomAD constraint

pLI —, LoF o/e 1.07

Max pathogenic AF

—

Genomic locus

chr15:41,828,095-41,848,155

External References & Databases

Ensembl (ENSG00000168970)

NCBI Gene (8681)

HGNC:34449

GenCC

ClinVar (JMJD7-PLA2G4B)

Transcript & Mutation Effects

hg38 • Region Span ~20.1 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to JMJD7-PLA2G4B variants in ClinVar

3 Conditions Cataloged

Inborn genetic diseasesTotal: 10

not providedTotal: 6

Neurodevelopmental disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript . Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar	1 clinvar	3
missense			7 clinvar		2 clinvar	9
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)					1 clinvar	1
Total	0	0	7	2	4	13

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001198588.2	RefSeq	NP_001185517.1	24	Standard
NM_005090.4	RefSeq	NP_005081.1	25	Standard
ENST00000342159.6	Ensembl	ENSP00000342785.4	24	Standard
ENST00000382448.8	Ensembl	ENSP00000371886.4	25	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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)

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000382448
Coding exons: 25
Length: 20061
Individuals with no LoFs: 125344
Homozygous LoFs: 0
Heterozygous LoFs: 404
Defined: 125748
p: 0.00161

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.99	744	606	1.23	0.0000377	6479
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0048	0.0046	notable
Latino/Admixed American	0.0017	0.0017	notable
Ashkenazi Jewish	0.00031	0.00030	rare
East Asian	0.0024	0.0023	notable
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.0010	0.00098	notable
South Asian	0.0034	0.0033	notable
Other	0.0015	0.0015	notable

dbNSFP Gene Annotations

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}.;

Intolerance Scores

RVIS EVS: 0.49
RVIS percentile EVS: 79.48

Essentials

Essential (CRISPR): N
Indispensability pred.: N
Indispensability score: 0.0914