JMJD7

protein-coding

jumonji domain containing 7, the group of Iron (II) and 2-oxoglutarate dependent oxygenases

Gene summary

This gene encodes a highly conserved protein with a JmjC domain, which are part of the cupin metalloenzyme superfamily. JmjC proteins may function as 2-oxoglutarate-Fe(II)-dependent dioxygenases. Most tissues also express read-through transcripts from this gene into the downstream phospholipase A2, group IVB (cytosolic) gene, some of which may encode fusion proteins combining the N-terminus of this protein with the phospholipase A2, group IVB protein. [provided by RefSeq, Jul 2008]

MANE transcript

NM_001114632.2

Inheritance

—

ClinVar variants

U:22B:7

Top phenotype

JMJD7-related disorder

gnomAD constraint

pLI —, LoF o/e 0.55

Max pathogenic AF

—

Genomic locus

chr15:41,828,092-41,837,581

External References & Databases

Ensembl (ENSG00000243789)

NCBI Gene (100137047)

Transcript & Mutation Effects

hg38 • Region Span ~9.5 kb

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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 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 23

JMJD7-related disorderTotal: 4

not providedTotal: 3

JMJD7-PLA2G4B-related disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001114632.2. 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	2 clinvar	4
missense			22 clinvar	2 clinvar	1 clinvar	25
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	22	4	3	29

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 14 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001114632.2	RefSeq	NP_001108104.1	8	MANE Select
ENST00000397299.9	Ensembl	ENSP00000380467.4	8	MANE Select
ENST00000408047.5	Ensembl	ENSP00000384174.1	6	Standard
ENST00000408047.6	Ensembl	ENSP00000384174.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding
2-oxoglutarate-dependent dioxygenase activity

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000397299
Coding exons: 8
Length: 9497
Individuals with no LoFs: 125682
Homozygous LoFs: 0
Heterozygous LoFs: 53
Defined: 125735
p: 0.000211

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.921	228	192	1.19	0.0000119	2015
Missense (PolyPhen)		87	73.181	1.1888		755
Synonymous	0.0135	86	86.2	0.998	0.00000596	633
Loss of Function	1.67	9	16.3	0.554	7.00e-7	184

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000066	0.000062	rare
Latino/Admixed American	0.00017	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0015	0.0015	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0.00013	0.00012	rare
South Asian	0.00017	0.00016	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.103

Intolerance Scores

LoFtool: 0.475
RVIS EVS: 0.55
RVIS percentile EVS: 81.6

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.121

Gene Damage Prediction

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