JMJD7

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

Basic information

Region (hg38): 15:41828092-41837581

Links

ENSG00000243789 ∙ NCBI:100137047 ∙ ∙ HGNC:34397 ∙ Uniprot:P0C870 ∙ AlphaFold ∙ 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 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the JMJD7 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			8	2	3	13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				2		2
Total	0	0	8	6	4

Variants in JMJD7

This is a list of pathogenic ClinVar variants found in the JMJD7 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)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
JMJD7	protein_coding	protein_coding	ENST00000397299	8	9497

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000816	0.932	125682	0	53	125735	0.000211

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.921	228	192	1.19	0.0000119	2015
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000240	0.000235
Ashkenazi Jewish	0.00	0.00
East Asian	0.00151	0.00147
Finnish	0.00	0.00
European (Non-Finnish)	0.000126	0.000123
Middle Eastern	0.00151	0.00147
South Asian	0.000169	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.475
• rvis_EVS: 0.55
• rvis_percentile_EVS: 81.6

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.518
• ghis: 0.496

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.121

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Jmjd7

Gene ontology

• Molecular function: protein binding;2-oxoglutarate-dependent dioxygenase activity