EIF2AK4

protein-coding

eukaryotic 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

NM_001013703.4

Inheritance

AR, AD

ClinVar variants

P:85U:194B:98

Top phenotype

Pulmonary venoocclusive disease 2

gnomAD constraint

pLI —, LoF o/e 0.44

Max pathogenic AF

—

Genomic locus

chr15:39,934,115-40,035,591

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~101.5 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

pulmonary venoocclusive disease 2STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0009329

Submitter: Labcorp Genetics (formerly Invitae)

pulmonary venoocclusive disease 2STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0009329

Submitter: PanelApp Australia

pulmonary veno-occlusive disease and/or pulmonary capillary haemangiomatosisDEFINITIVE

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).

pulmonary venoocclusive disease 2SUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0009329

Submitter: Orphanet

heritable pulmonary arterial hypertensionSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0017148

Submitter: Orphanet

pulmonary venoocclusive diseaseSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0009937

Submitter: Orphanet

Clinical Genomic Database (CGD)

Pulmonary venoocclusive disease 2AR

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

Refs: 24292273Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to EIF2AK4 variants in ClinVar

9 Conditions Cataloged
not providedTotal: 235
Inborn genetic diseasesTotal: 134
Familial pulmonary capillary hemangiomatosisTotal: 98
not specifiedTotal: 39
EIF2AK4-related disorderTotal: 25
EIF2AK4-related disordersTotal: 11
Pulmonary arterial hypertensionTotal: 4
EBV-positive nodal T- and NK-cell lymphomaTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
1
clinvar
63
clinvar
3
clinvar
68
missense
2
clinvar
7
clinvar
182
clinvar
30
clinvar
2
clinvar
223
nonsense
19
clinvar
7
clinvar
1
clinvar
27
start loss
0
frameshift
24
clinvar
13
clinvar
2
clinvar
39
splice donor/acceptor (+/-2bp)
7
clinvar
5
clinvar
8
clinvar
20
Total5332194935377

Highest pathogenic variant AF is 0.00014604781

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 38 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001013703.4RefSeqNP_001013725.239MANE Select
ENST00000263791.10EnsemblENSP00000263791.539MANE Select
ENST00000558823.1EnsemblENSP00000454210.13Standard
ENST00000559624.5EnsemblENSP00000453148.111Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense2.676809060.7510.000049610800
Missense (PolyPhen)168281.750.596273413
Synonymous0.5003353470.9660.00001983108
Loss of Function5.044295.00.4420.000005061125

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000520.00050rare
Latino/Admixed American0.000260.00026rare
Ashkenazi Jewish0.000200.00020rare
East Asian0.000790.00078rare
Finnish0.000190.00019rare
European (Non-Finnish)0.00110.0011notable
South Asian0.000500.00049rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumHigh
CancerMediumMediumMedium
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