NOD1

nucleotide binding oligomerization domain containing 1, the group of Caspase recruitment domain containing|NLR family

Basic information

Region (hg38): 7:30424526-30478784

Previous symbols: [ "CARD4" ]

Links

ENSG00000106100 ∙ NCBI:10392 ∙ OMIM:605980 ∙ HGNC:16390 ∙ Uniprot:Q9Y239 ∙ 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 NOD1 gene.

• Inborn genetic diseases (41 variants)
• not provided (36 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NOD1 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				2	3	5
missense			37	6	3	46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	37	9	6

Variants in NOD1

This is a list of pathogenic ClinVar variants found in the NOD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-30425649-T-G		not specified	Uncertain significance (Oct 30, 2023)
7-30425672-A-C		not specified	Uncertain significance (Nov 30, 2021)
7-30425677-G-C			Benign (Dec 11, 2017)
7-30425696-A-C		not specified	Uncertain significance (Jun 21, 2023)
7-30433104-C-G			not provided (-)
7-30433124-T-C		not specified	Uncertain significance (Jun 06, 2023)
7-30437179-A-T			not provided (-)
7-30437229-G-C			not provided (-)
7-30437404-T-G			not provided (-)
7-30437492-C-T			not provided (-)
7-30437613-C-T		not specified	Uncertain significance (Nov 15, 2021)
7-30437772-C-G			not provided (-)
7-30446154-T-C		not specified	Uncertain significance (Jan 19, 2024)
7-30446159-T-C		not specified	Uncertain significance (Dec 13, 2023)
7-30446976-G-A			Likely benign (Dec 01, 2022)
7-30447010-C-T		not specified	Likely benign (Jun 29, 2023)
7-30447017-G-C			Likely benign (Aug 15, 2018)
7-30447028-C-G		not specified	Uncertain significance (Mar 24, 2023)
7-30447926-A-T			not provided (-)
7-30448078-A-T			not provided (-)
7-30448180-G-A			not provided (-)
7-30448186-C-T			not provided (-)
7-30448208-C-T			not provided (-)
7-30448267-A-G			not provided (-)
7-30448408-G-A			not provided (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NOD1	protein_coding	protein_coding	ENST00000222823	11	54258

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.46e-18	0.0286	125399	2	347	125748	0.00139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.119	566	574	0.986	0.0000371	6246
Missense in Polyphen		209	216.62	0.96484		2404
Synonymous	-0.196	262	258	1.02	0.0000171	1942
Loss of Function	0.772	30	34.9	0.859	0.00000158	402

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00115	0.00115
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000272	0.000272
Finnish	0.00901	0.00896
European (Non-Finnish)	0.000863	0.000827
Middle Eastern	0.000272	0.000272
South Asian	0.000490	0.000490
Other	0.000978	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Enhances caspase-9-mediated apoptosis. Induces NF-kappa- B activity via RIPK2 and IKK-gamma. Confers responsiveness to intracellular bacterial lipopolysaccharides (LPS). Forms an intracellular sensing system along with ARHGEF2 for the detection of microbial effectors during cell invasion by pathogens. Required for RHOA and RIPK2 dependent NF-kappa-B signaling pathway activation upon S.flexneri cell invasion. Involved not only in sensing peptidoglycan (PGN)-derived muropeptides but also in the activation of NF-kappa-B by Shigella effector proteins IpgB2 and OspB. Recruits NLRP10 to the cell membrane following bacterial infection. {ECO:0000269|PubMed:11058605, ECO:0000269|PubMed:17054981, ECO:0000269|PubMed:19043560, ECO:0000269|PubMed:22672233}.
• Pathway: Pertussis - Homo sapiens (human);Epithelial cell signaling in Helicobacter pylori infection - Homo sapiens (human);NOD-like receptor signaling pathway - Homo sapiens (human);Shigellosis - Homo sapiens (human);Nucleotide-binding Oligomerization Domain (NOD) pathway;Toll Like Receptor 7/8 (TLR7/8) Cascade;Interleukin-17 signaling;Signaling by Interleukins;Cytokine Signaling in Immune system;Toll Like Receptor 9 (TLR9) Cascade;MyD88 cascade initiated on plasma membrane;Toll Like Receptor 10 (TLR10) Cascade;Toll Like Receptor 3 (TLR3) Cascade;Toll Like Receptor 5 (TLR5) Cascade;Toll-Like Receptors Cascades;NOD1/2 Signaling Pathway;Nucleotide-binding domain, leucine rich repeat containing receptor (NLR) signaling pathways;Post-translational protein modification;Metabolism of proteins;Interleukin-1 signaling;Innate Immune System;Immune System;TAK1 activates NFkB by phosphorylation and activation of IKKs complex;JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1;activated TAK1 mediates p38 MAPK activation;MAP kinase activation;TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation;MyD88 dependent cascade initiated on endosome;Ovarian tumor domain proteases;Deubiquitination;TRIF(TICAM1)-mediated TLR4 signaling ;MyD88-independent TLR4 cascade ;Toll Like Receptor 4 (TLR4) Cascade;MyD88:Mal cascade initiated on plasma membrane;Toll Like Receptor TLR1:TLR2 Cascade;Toll Like Receptor TLR6:TLR2 Cascade;Toll Like Receptor 2 (TLR2) Cascade;Interleukin-1 family signaling (Consensus)

Recessive Scores

• pRec: 0.261

Intolerance Scores

• loftool: 0.857
• rvis_EVS: -0.46
• rvis_percentile_EVS: 23.73

Haploinsufficiency Scores

• pHI: 0.0928
• hipred: Y
• hipred_score: 0.564
• ghis: 0.515

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.773

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nod1
• Phenotype: immune system phenotype; hematopoietic system phenotype

Zebrafish Information Network

• Gene name: nod1
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: viability

Gene ontology

• Biological process: activation of MAPK activity;positive regulation of dendritic cell antigen processing and presentation;apoptotic process;activation of cysteine-type endopeptidase activity involved in apoptotic process;defense response;inflammatory response;signal transduction;JNK cascade;detection of biotic stimulus;detection of bacterium;positive regulation of interleukin-1 beta production;positive regulation of interleukin-6 production;positive regulation of tumor necrosis factor production;intracellular signal transduction;interleukin-8 biosynthetic process;defense response to bacterium;positive regulation of I-kappaB kinase/NF-kappaB signaling;positive regulation of cysteine-type endopeptidase activity involved in apoptotic process;innate immune response;positive regulation of JNK cascade;defense response to Gram-positive bacterium;positive regulation of nitric-oxide synthase activity;positive regulation of NF-kappaB transcription factor activity;protein complex oligomerization;positive regulation of ERK1 and ERK2 cascade;nucleotide-binding oligomerization domain containing signaling pathway;interleukin-1-mediated signaling pathway;cellular response to muramyl dipeptide;positive regulation of NIK/NF-kappaB signaling;positive regulation of xenophagy
• Cellular component: cytoplasm;cytosol;basolateral plasma membrane;apical plasma membrane
• Molecular function: protein binding;ATP binding;cysteine-type endopeptidase activator activity involved in apoptotic process;identical protein binding;protein homodimerization activity;peptidoglycan binding;protein-containing complex binding;CARD domain binding