ETNK2
protein-codingethanolamine kinase 2
Gene summary
The protein encoded by this gene is a member of choline/ethanolamine kinase family which catalyzes the first step of phosphatidylethanolamine (PtdEtn) biosynthesis via the cytidine diphosphate (CDP) ethanolamine pathway. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~21.0 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 ETNK2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_018208.4. 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 | 1 | 3 | ||
| missense | 44 | 2 | 46 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 46 | 3 | 1 | 50 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_060678.2 | 8 | MANE Select | |
| Ensembl | ENSP00000356170.4 | 8 | MANE Select | |
| RefSeq | NP_001284689.1 | 7 | Standard | |
| RefSeq | NP_001284690.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Glycerophospholipid metabolism - Homo sapiens (human)
- Glucocorticoid Receptor Pathway
- Nuclear Receptors Meta-Pathway
- Kennedy pathway from Sphingolipids
- One carbon metabolism and related pathways
Biological Process
- in utero embryonic development
- placenta development
- phosphatidylethanolamine biosynthetic process
- biological_process
- post-embryonic development
Molecular Function
- ethanolamine kinase activity
- ATP binding
Cellular Component
- cellular_component
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000367202
- Coding exons
- 8
- Length
- 21118
- Individuals with no LoFs
- 125596
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 13
- Defined
- 125609
- p
- 0.0000517
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.10 | 170 | 215 | 0.790 | 0.0000122 | 2503 |
| Missense (PolyPhen) | 63 | 79.508 | 0.79238 | 950 | ||
| Synonymous | 0.119 | 88 | 89.4 | 0.984 | 0.00000529 | 712 |
| Loss of Function | 1.33 | 12 | 18.1 | 0.663 | 7.70e-7 | 215 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.000058 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000071 | 0.000070 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Highly specific for ethanolamine phosphorylation. Does not have choline kinase activity (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.0835
Intolerance Scores
- LoFtool
- 0.342
- RVIS EVS
- 0.02
- RVIS percentile EVS
- 55.22
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.998
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |