JMJD8
protein-codingjumonji domain containing 8
Gene summary
Predicted to enable cis-regulatory region sequence-specific DNA binding activity. Involved in several processes, including positive regulation of canonical NF-kappaB signal transduction; positive regulation of sprouting angiogenesis; and regulation of pyruvate kinase activity. Located in endoplasmic reticulum lumen and nucleus. [provided by Alliance of Genome Resources, Jul 2025]
- C16orf20
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~2.9 kbGenCC 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 JMJD8 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001005920.4. 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 | 1 | 1 | ||||
| missense | 86 | 2 | 88 | |||
| nonsense | 0 | |||||
| start loss | 1 | 1 | ||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 7 | 7 | ||||
| Total | 0 | 0 | 94 | 3 | 0 | 97 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001005920.3 | 9 | MANE Select | |
| Ensembl | ENSP00000477481.1 | 9 | MANE Select | |
| RefSeq | NP_001310847.2 | 9 | Standard | |
| RefSeq | NP_001310848.2 | 8 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- regulation of glycolytic process
- positive regulation of I-kappaB kinase/NF-kappaB signaling
- regulation of pyruvate kinase activity
- positive regulation of sprouting angiogenesis
Molecular Function
- protein binding
Cellular Component
- nucleus
- cytoplasm
- endoplasmic reticulum
- endoplasmic reticulum lumen
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000412368
- Coding exons
- 9
- Length
- 2859
- Individuals with no LoFs
- 124521
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 37
- Defined
- 124558
- p
- 0.000149
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -1.92 | 224 | 156 | 1.43 | 0.00000914 | 1741 |
| Missense (PolyPhen) | 74 | 62.365 | 1.1866 | 629 | ||
| Synonymous | -3.61 | 107 | 68.9 | 1.55 | 0.00000419 | 590 |
| Loss of Function | -0.954 | 18 | 14.1 | 1.27 | 6.03e-7 | 172 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00037 | 0.00032 | rare |
| Latino/Admixed American | 0.00015 | 0.00014 | rare |
| Ashkenazi Jewish | 0.00030 | 0.00030 | rare |
| East Asian | 0.00017 | 0.00017 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00017 | 0.00017 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Functions as a positive regulator of TNF-induced NF- kappa-B signaling (PubMed:27671354). Regulates angiogenesis and cellular metabolism through interaction with PKM (PubMed:27199445). {ECO:0000269|PubMed:27199445, ECO:0000269|PubMed:27671354}.;
Intolerance Scores
- LoFtool
- 0.579
- RVIS EVS
- 0.88
- RVIS percentile EVS
- 89.07
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.235
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |