GeneBe

NLRX1

NLR family member X1, the group of NLR family

Basic information

Region (hg38): 11:119166568-119184016

Links

ENSG00000160703 ∙ NCBI:79671 ∙ OMIM:611947 ∙ HGNC:29890 ∙ Uniprot:Q86UT6 ∙ 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 NLRX1 gene.

  • not_specified (157 variants)
  • not_provided (29 variants)
  • Long_QT_syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NLRX1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001282144.2. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
4
clinvar
1
clinvar
1
clinvar
 6
missense
158
clinvar
8
clinvar
2
clinvar
 168
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
1
clinvar
 1
Total 0 0 163 9 3
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
NLRX1protein_codingprotein_codingENST00000409109 917449
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
7.73e-310.0000032412533714101257480.00164
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.1346046130.9850.00004276192
Missense in Polyphen189204.790.922892345
Synonymous0.4292512600.9660.00001632210
Loss of Function-1.074235.21.190.00000219346

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.004810.00475
Ashkenazi Jewish0.000.00
East Asian0.0003820.000381
Finnish0.001300.00129
European (Non-Finnish)0.001180.00116
Middle Eastern0.0003820.000381
South Asian0.004350.00432
Other0.0003270.000326

dbNSFP

Source: dbNSFP

Function
FUNCTION: Participates in antiviral signaling. Acts as a negative regulator of MAVS-mediated antiviral responses, through the inhibition of the virus-induced RLH (RIG-like helicase)-MAVS interaction (PubMed:18200010). Instead, promotes autophagy by interacting with TUFM and subsequently recruiting the autophagy- related proteins ATG5 and ATG12 (PubMed:22749352). Regulates also MAVS-dependent NLRP3 inflammasome activation to attenuate apoptosis (PubMed:27393910). Has no inhibitory function on NF- kappa-B signaling pathway, but enhances NF-kappa-B and JUN N- terminal kinase dependent signaling through the production of reactive oxygen species (PubMed:18219313). {ECO:0000269|PubMed:18200010, ECO:0000269|PubMed:18219313, ECO:0000269|PubMed:22749352, ECO:0000269|PubMed:27393910}.;
Pathway
Influenza A - Homo sapiens (human);NOD-like receptor signaling pathway - Homo sapiens (human);RIG-I-like receptor signaling pathway - Homo sapiens (human);RIG-I-like Receptor Signaling;DDX58/IFIH1-mediated induction of interferon-alpha/beta;Innate Immune System;Immune System;Negative regulators of DDX58/IFIH1 signaling (Consensus)

Recessive Scores

pRec
0.134

Intolerance Scores

loftool
0.946
rvis_EVS
0.19
rvis_percentile_EVS
66.58

Haploinsufficiency Scores

pHI
0.0945
hipred
N
hipred_score
0.197
ghis
0.467

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.564

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Nlrx1
Phenotype
homeostasis/metabolism phenotype; growth/size/body region phenotype; immune system phenotype; hematopoietic system phenotype;

Gene ontology

Biological process
viral process;negative regulation of type I interferon production;negative regulation of interferon-beta production;negative regulation of interleukin-6 production;intracellular signal transduction;negative regulation of RIG-I signaling pathway;negative regulation of I-kappaB kinase/NF-kappaB signaling;innate immune response;negative regulation of innate immune response;negative regulation of inflammatory response
Cellular component
cytoplasm;mitochondrion;mitochondrial outer membrane;plasma membrane;cell junction
Molecular function
protein binding;ATP binding