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.

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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	1	2
missense			67	2	2	71
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	67	3	3

Variants in NLRX1

This is a list of pathogenic ClinVar variants found in the NLRX1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-119168034-G-A			not provided (-)
11-119168321-G-A			not provided (-)
11-119168342-T-C			not provided (-)
11-119168442-C-T			not provided (-)
11-119168581-C-T			not provided (-)
11-119168682-T-C			not provided (-)
11-119171357-A-G			not provided (-)
11-119171367-G-C			not provided (-)
11-119171428-A-G		not specified	Uncertain significance (Oct 05, 2023)
11-119171716-G-C			not provided (-)
11-119171728-G-A			not provided (-)
11-119172362-G-A			Benign (May 30, 2018)
11-119172416-G-A		not specified	Uncertain significance (Oct 26, 2021)
11-119172685-G-A			not provided (-)
11-119172954-G-T		not specified	Uncertain significance (Dec 18, 2023)
11-119173359-T-C			not provided (-)
11-119173368-C-T			not provided (-)
11-119173387-G-A			not provided (-)
11-119173388-T-C			not provided (-)
11-119173500-G-T		not specified	Uncertain significance (Jul 14, 2021)
11-119173524-G-A		not specified	Uncertain significance (Jun 21, 2022)
11-119173541-C-T		not specified	Uncertain significance (May 03, 2023)
11-119173557-C-G		not specified	Uncertain significance (Mar 07, 2024)
11-119173580-G-A		not specified	Uncertain significance (Apr 22, 2024)
11-119173596-G-A		not specified	Uncertain significance (Apr 15, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NLRX1	protein_coding	protein_coding	ENST00000409109	9	17449

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.73e-31	0.00000324	125337	1	410	125748	0.00164

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.134	604	613	0.985	0.0000427	6192
Missense in Polyphen		189	204.79	0.92289		2345
Synonymous	0.429	251	260	0.966	0.0000163	2210
Loss of Function	-1.07	42	35.2	1.19	0.00000219	346

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00481	0.00475
Ashkenazi Jewish	0.00	0.00
East Asian	0.000382	0.000381
Finnish	0.00130	0.00129
European (Non-Finnish)	0.00118	0.00116
Middle Eastern	0.000382	0.000381
South Asian	0.00435	0.00432
Other	0.000327	0.000326

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

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