JMJD4

jumonji domain containing 4, the group of JmjC hydroxylases

Basic information

Region (hg38): 1:227730424-227735411

Links

ENSG00000081692 ∙ NCBI:65094 ∙ ∙ HGNC:25724 ∙ Uniprot:Q9H9V9 ∙ 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 JMJD4 gene.

• Inborn genetic diseases (23 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the JMJD4 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					1	1
missense			21			21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1	1		2
Total	0	0	22	1	1

Variants in JMJD4

This is a list of pathogenic ClinVar variants found in the JMJD4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-227732428-C-A		not specified	Uncertain significance (Feb 13, 2024)
1-227732435-A-T		not specified	Uncertain significance (Oct 27, 2022)
1-227732463-C-T		not specified	Uncertain significance (Oct 25, 2022)
1-227732487-C-T		not specified	Uncertain significance (Mar 04, 2024)
1-227732495-G-A		not specified	Uncertain significance (Sep 27, 2021)
1-227732499-C-T		not specified	Uncertain significance (Jul 09, 2021)
1-227732514-C-T		not specified	Uncertain significance (Apr 25, 2022)
1-227732516-T-C		not specified	Uncertain significance (Sep 14, 2023)
1-227732525-C-T		not specified	Uncertain significance (Nov 29, 2023)
1-227732625-G-A		not specified	Uncertain significance (Apr 12, 2022)
1-227732660-C-G		not specified	Uncertain significance (Mar 11, 2022)
1-227732903-G-T		not specified	Uncertain significance (Apr 22, 2022)
1-227732967-G-A		Inborn genetic diseases	Uncertain significance (Dec 07, 2021)
1-227733027-C-A		not specified	Uncertain significance (Mar 07, 2024)
1-227733508-C-T		not specified	Uncertain significance (Jan 29, 2024)
1-227733552-G-A			Benign (Feb 13, 2018)
1-227733561-G-T		not specified	Uncertain significance (Jan 23, 2023)
1-227733565-C-T		not specified	Uncertain significance (Oct 31, 2023)
1-227733920-G-T		not specified	Uncertain significance (Jan 19, 2022)
1-227733925-G-A		not specified	Uncertain significance (Apr 13, 2022)
1-227733926-C-A		not specified	Uncertain significance (Jan 23, 2024)
1-227733982-T-C		not specified	Uncertain significance (Dec 02, 2022)
1-227734024-G-A		not specified	Uncertain significance (Dec 18, 2023)
1-227734693-G-A		not specified	Uncertain significance (Jun 13, 2022)
1-227734718-C-T		not specified	Uncertain significance (Oct 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
JMJD4	protein_coding	protein_coding	ENST00000366758	6	4987

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.49e-9	0.210	125513	0	218	125731	0.000867

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.841	307	268	1.14	0.0000152	2981
Missense in Polyphen		40	43.683	0.91568		537
Synonymous	-1.68	144	120	1.20	0.00000772	935
Loss of Function	0.556	15	17.5	0.857	7.61e-7	169

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00112	0.00111
Ashkenazi Jewish	0.000432	0.000397
East Asian	0.000224	0.000217
Finnish	0.000162	0.000139
European (Non-Finnish)	0.00107	0.000968
Middle Eastern	0.000224	0.000217
South Asian	0.00214	0.00203
Other	0.000183	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.931
• rvis_EVS: 0.04
• rvis_percentile_EVS: 57.15

Haploinsufficiency Scores

• pHI: 0.135
• hipred: N
• hipred_score: 0.170
• ghis: 0.534

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.447

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Jmjd4

Gene ontology

• Molecular function: protein binding