EIF2AK4
protein-codingeukaryotic translation initiation factor 2 alpha kinase 4, the group of Eukaryotic translation initiation factor 2 alpha kinases
Gene summary
This gene encodes a member of a family of kinases that phosphorylate the alpha subunit of eukaryotic translation initiation factor-2 (EIF2), resulting in the downregulaton of protein synthesis. The encoded protein responds to amino acid deprivation by binding uncharged transfer RNAs. It may also be activated by glucose deprivation and viral infection. Mutations in this gene have been found in individuals suffering from autosomal recessive pulmonary venoocclusive-disease-2. [provided by RefSeq, Mar 2014]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~101.5 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0009329
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0009329
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0018554
Submitter: ClinGen
EIF2AK4 was first reported in relation to autosomal recessive pulmonary veno-occlusive disease (PVOD) in 2014 (Eyries et al., PMID:24292273). More than 22 distinct variants (e.g. missense, in-frame indel, nonsense, frameshift, etc) have been reported in humans. Evidence supporting this gene-disease relationship includes case-level genetic data and protein expression in lung. Summary of case-level data: 43.4 points (max. 12 points) variants in this gene have been reported in more than 21 probands (PMIDs: 24292273, 24135949, 25512148, 28972005, and others). Summary of experimental evidence: 0.5 points. The evidence supporting this gene-disease relationship has been replicated over more than 5 years. In summary, EIF2AK4 is definitively associated with autosomal recessive pulmonary veno-occlusive disease/capillary haemangiomatosis (PVOD/PCH) which is frequently misdiagnosed as pulmonary arterial hypertension. This classification was approved by the ClinGen PH Gene Curation Expert Panel on August 30, 2022 (SOP v9).
Inheritance Pattern: AD
Disease ID:MONDO:0009329
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0017148
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0009937
Submitter: Orphanet
Clinical Genomic Database (CGD)
Manifestation: Cardiovascular; Pulmonary
Intervention: Cardiovascular; Pulmonary
Rationale: Medical treatment (eg, with calcium antagonists, anticoagulants, prostanoids, endothelin receptor antagonists, etc.) may be beneficial, though lung transplantation may be required
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to EIF2AK4 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001013703.4. 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 | 63 | 3 | 68 | |
| missense | 2 | 7 | 182 | 30 | 2 | 223 |
| nonsense | 19 | 7 | 1 | 27 | ||
| start loss | 0 | |||||
| frameshift | 24 | 13 | 2 | 39 | ||
| splice donor/acceptor (+/-2bp) | 7 | 5 | 8 | 20 | ||
| Total | 53 | 32 | 194 | 93 | 5 | 377 |
Highest pathogenic variant AF is 0.00014604781
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001013725.2 | 39 | MANE Select | |
| Ensembl | ENSP00000263791.5 | 39 | MANE Select | |
| Ensembl | ENSP00000454210.1 | 3 | Standard | |
| Ensembl | ENSP00000453148.1 | 11 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Influenza A - Homo sapiens (human)
- Protein processing in endoplasmic reticulum - Homo sapiens (human)
- Autophagy - animal - Homo sapiens (human)
- Hepatitis C - Homo sapiens (human)
- Measles - Homo sapiens (human)
Biological Process
- DNA damage checkpoint
- positive regulation of defense response to virus by host
- adaptive immune response
- T cell activation involved in immune response
- positive regulation of adaptive immune response
Molecular Function
- tRNA binding
- protein kinase activity
- protein serine/threonine kinase activity
- eukaryotic translation initiation factor 2alpha kinase activity
- ATP binding
Cellular Component
- polysome
- cytosolic ribosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000263791
- Coding exons
- 39
- Length
- 101451
- Individuals with no LoFs
- 125005
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 180
- Defined
- 125185
- p
- 0.000719
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.67 | 680 | 906 | 0.751 | 0.0000496 | 10800 |
| Missense (PolyPhen) | 168 | 281.75 | 0.59627 | 3413 | ||
| Synonymous | 0.500 | 335 | 347 | 0.966 | 0.0000198 | 3108 |
| Loss of Function | 5.04 | 42 | 95.0 | 0.442 | 0.00000506 | 1125 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00052 | 0.00050 | rare |
| Latino/Admixed American | 0.00026 | 0.00026 | rare |
| Ashkenazi Jewish | 0.00020 | 0.00020 | rare |
| East Asian | 0.00079 | 0.00078 | rare |
| Finnish | 0.00019 | 0.00019 | rare |
| European (Non-Finnish) | 0.0011 | 0.0011 | notable |
| South Asian | 0.00050 | 0.00049 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Metabolic-stress sensing protein kinase that phosphorylates the alpha subunit of eukaryotic translation initiation factor 2 (eIF-2-alpha/EIF2S1) on 'Ser-52' in response to low amino acid availability (PubMed:25329545). Plays a role as an activator of the integrated stress response (ISR) required for adapatation to amino acid starvation. Converts phosphorylated eIF- 2-alpha/EIF2S1 either to a competitive inhibitor of the translation initiation factor eIF-2B, leading to a global protein synthesis repression, and thus to a reduced overall utilization of amino acids, or to a translational initiation activation of specific mRNAs, such as the transcriptional activator ATF4, and hence allowing ATF4-mediated reprogramming of amino acid biosynthetic gene expression to alleviate nutrient depletion. Binds uncharged tRNAs (By similarity). Involved in cell cycle arrest by promoting cyclin D1 mRNA translation repression after the unfolded protein response pathway (UPR) activation or cell cycle inhibitor CDKN1A/p21 mRNA translation activation in response to amino acid deprivation (PubMed:26102367). Plays a role in the consolidation of synaptic plasticity, learning as well as formation of long-term memory. Plays a role in neurite outgrowth inhibition. Plays a proapoptotic role in response to glucose deprivation. Promotes global cellular protein synthesis repression in response to UV irradiation independently of the stress- activated protein kinase/c-Jun N-terminal kinase (SAPK/JNK) and p38 MAPK signaling pathways (By similarity). Plays a role in the antiviral response against alphavirus infection; impairs early viral mRNA translation of the incoming genomic virus RNA, thus preventing alphavirus replication (By similarity). {ECO:0000250|UniProtKB:P15442, ECO:0000250|UniProtKB:Q9QZ05, ECO:0000269|PubMed:25329545, ECO:0000269|PubMed:26102367}.;
- Disease
- DISEASE: Pulmonary venoocclusive disease 2, autosomal recessive (PVOD2) [MIM:234810]: A disease characterized by widespread fibrous obstruction and intimal thickening of septal veins and preseptal venules, a low diffusing capacity for carbon monoxide, occult alveolar hemorrhage, and nodular ground-glass opacities, septal lines and lymph node enlargement showed by high-resolution computed tomography of the chest. It is frequently associated with pulmonary capillary dilatation and proliferation, and is a rare and devastating cause of pulmonary hypertension. {ECO:0000269|PubMed:24135949, ECO:0000269|PubMed:24292273}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Intolerance Scores
- LoFtool
- 0.866
- RVIS EVS
- -0.72
- RVIS percentile EVS
- 14.27
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.697
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |