NLRC5

NLR family CARD domain containing 5, the group of NLR family

Basic information

Region (hg38): 16:56989484-57083531

Links

ENSG00000140853 ∙ NCBI:84166 ∙ OMIM:613537 ∙ HGNC:29933 ∙ Uniprot:Q86WI3 ∙ 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 NLRC5 gene.

• Inborn genetic diseases (76 variants)
• not provided (75 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NLRC5 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				4	2	6
missense			72	8	2	82
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding						0
Total	0	0	72	12	4

Variants in NLRC5

This is a list of pathogenic ClinVar variants found in the NLRC5 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-57020544-T-C			not provided (-)
16-57020726-G-T		not specified	Uncertain significance (Oct 14, 2021)
16-57020780-A-C		not specified	Uncertain significance (Aug 02, 2022)
16-57020800-G-A		not specified	Uncertain significance (Sep 01, 2021)
16-57020828-C-T		not specified	Likely benign (Mar 31, 2022)
16-57020838-T-G		not specified	Uncertain significance (Apr 13, 2022)
16-57020848-G-A		not specified	Uncertain significance (Sep 14, 2022)
16-57020867-A-G		not specified	Uncertain significance (Jun 09, 2022)
16-57020990-C-G		not specified	Uncertain significance (Jun 28, 2022)
16-57022227-A-C			not provided (-)
16-57023663-C-T			not provided (-)
16-57023697-G-A			not provided (-)
16-57023899-C-G			not provided (-)
16-57024091-C-T			not provided (-)
16-57024129-C-T			not provided (-)
16-57025406-G-A		not specified	Uncertain significance (May 11, 2022)
16-57025419-A-G		not specified	Uncertain significance (Aug 08, 2023)
16-57025425-G-A		not specified	Uncertain significance (Oct 26, 2022)
16-57025493-G-A		not specified	Uncertain significance (May 26, 2022)
16-57025538-G-A		not specified	Uncertain significance (Jul 20, 2021)
16-57025539-T-C		not specified	Uncertain significance (Sep 01, 2021)
16-57025557-C-T		not specified	Uncertain significance (Sep 13, 2023)
16-57025602-G-A		not specified	Uncertain significance (May 10, 2022)
16-57025605-C-T		not specified	Uncertain significance (Jun 22, 2021)
16-57025661-C-T			Likely benign (Sep 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NLRC5	protein_coding	protein_coding	ENST00000262510	47	94047

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.42e-8	1.00	125677	0	71	125748	0.000282

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.01	837	1.02e+3	0.823	0.0000582	12102
Missense in Polyphen		101	185.24	0.54524		2596
Synonymous	0.748	424	444	0.955	0.0000268	3816
Loss of Function	5.90	30	90.6	0.331	0.00000430	1062

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000548	0.000544
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.000436	0.000416
European (Non-Finnish)	0.000360	0.000352
Middle Eastern	0.000163	0.000163
South Asian	0.000164	0.000163
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable regulator of the NF-kappa-B and type I interferon signaling pathways. May also regulate the type II interferon signaling pathway. Plays a role in homeostatic control of innate immunity and in antiviral defense mechanisms. {ECO:0000269|PubMed:20061403, ECO:0000269|PubMed:20434986}.
• Pathway: DDX58/IFIH1-mediated induction of interferon-alpha/beta;Innate Immune System;Immune System;Negative regulators of DDX58/IFIH1 signaling (Consensus)

Recessive Scores

• pRec: 0.0897

Intolerance Scores

• rvis_EVS: 0.51
• rvis_percentile_EVS: 80.3

Haploinsufficiency Scores

• pHI: 0.0793
• hipred: N
• hipred_score: 0.429
• ghis: 0.474

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.277

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nlrc5
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: response to bacterium;negative regulation of NF-kappaB transcription factor activity;negative regulation of type I interferon production;intracellular signal transduction;regulation of kinase activity;innate immune response;positive regulation of MHC class I biosynthetic process;positive regulation of transcription by RNA polymerase II;defense response to virus;positive regulation of interferon-gamma-mediated signaling pathway;negative regulation of type I interferon-mediated signaling pathway;positive regulation of type I interferon-mediated signaling pathway
• Cellular component: nucleus;cytoplasm;centrosome;cytosol
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;protein binding;ATP binding