NLRP10

NLR family pyrin domain containing 10, the group of Pyrin domain containing|NLR family

Basic information

Region (hg38): 11:7957536-7965447

Previous symbols: [ "NALP10" ]

Links

ENSG00000182261 ∙ NCBI:338322 ∙ OMIM:609662 ∙ HGNC:21464 ∙ Uniprot:Q86W26 ∙ 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 NLRP10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NLRP10 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					3	3
missense			36			36
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	1	3

Variants in NLRP10

This is a list of pathogenic ClinVar variants found in the NLRP10 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-7959664-G-A		not specified	Uncertain significance (Aug 16, 2021)
11-7959706-T-C		not specified	Uncertain significance (Dec 01, 2022)
11-7959725-A-G			not provided (-)
11-7959736-CCTT-C			not provided (-)
11-7959776-A-T			Benign (Apr 01, 2024)
11-7959964-C-T		not specified	Uncertain significance (Jan 24, 2024)
11-7960011-C-G		not specified	Uncertain significance (Feb 28, 2024)
11-7960033-A-C		not specified	Uncertain significance (May 31, 2023)
11-7960043-T-A		not specified	Uncertain significance (May 30, 2024)
11-7960090-C-T		not specified	Uncertain significance (Jan 03, 2024)
11-7960093-T-C		not specified	Uncertain significance (Dec 02, 2022)
11-7960202-C-T			not provided (-)
11-7960204-G-C		not specified	Uncertain significance (Dec 07, 2021)
11-7960231-A-G		not specified	Uncertain significance (Oct 27, 2021)
11-7960246-G-A		not specified	Uncertain significance (Jan 04, 2022)
11-7960261-C-T		not specified	Uncertain significance (Feb 16, 2023)
11-7960275-A-G		not specified	Uncertain significance (Mar 26, 2024)
11-7960324-C-T		not specified	Uncertain significance (Jun 18, 2021)
11-7960401-A-C		not specified	Uncertain significance (Nov 03, 2023)
11-7960444-A-G		not specified	Uncertain significance (Jan 03, 2024)
11-7960560-C-T		not specified	Uncertain significance (Dec 05, 2022)
11-7960573-G-C		not specified	Uncertain significance (Jan 02, 2024)
11-7960619-C-T			not provided (-)
11-7960678-T-G		not specified	Uncertain significance (Jul 12, 2022)
11-7960751-G-A			Benign (Feb 20, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NLRP10	protein_coding	protein_coding	ENST00000328600	2	6003

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.01e-8	0.178	125612	0	134	125746	0.000533

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.287	362	347	1.04	0.0000189	4293
Missense in Polyphen		63	61.924	1.0174		914
Synonymous	-1.20	167	148	1.13	0.00000832	1277
Loss of Function	0.309	13	14.3	0.912	6.88e-7	185

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000864	0.000857
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000144	0.000141
Middle Eastern	0.000272	0.000272
South Asian	0.00287	0.00288
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibits autoprocessing of CASP1, CASP1-dependent IL1B secretion, PYCARD aggregation and PYCARD-mediated apoptosis but not apoptosis induced by FAS or BID (PubMed:15096476). Displays anti-inflammatory activity (PubMed:20393137). Required for immunity against C.albicans infection (By similarity). Involved in the innate immune response by contributing to proinflammatory cytokine release in response to invasive bacterial infection (PubMed:22672233). Contributes to T-cell-mediated inflammatory responses in the skin (By similarity). Plays a role in protection against periodontitis through its involvement in induction of IL1A via ERK activation in oral epithelial cells infected with periodontal pathogens (PubMed:28766990). Exhibits both ATPase and GTPase activities (PubMed:23861819). {ECO:0000250|UniProtKB:Q8CCN1, ECO:0000269|PubMed:15096476, ECO:0000269|PubMed:20393137, ECO:0000269|PubMed:22672233, ECO:0000269|PubMed:23861819}.
• Pathway: Nucleotide-binding Oligomerization Domain (NOD) pathway (Consensus)

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.461
• rvis_EVS: 0.05
• rvis_percentile_EVS: 57.52

Haploinsufficiency Scores

• pHI: 0.115
• hipred: N
• hipred_score: 0.123
• ghis: 0.484

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.682

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nlrp10
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: adaptive immune response;positive regulation of T-helper 1 type immune response;inflammatory response;innate immune response;positive regulation of interleukin-1 alpha secretion;positive regulation of inflammatory response;defense response to Gram-negative bacterium;defense response to fungus;positive regulation of defense response to bacterium;positive regulation of T-helper 17 type immune response;positive regulation of interleukin-8 secretion;positive regulation of interleukin-6 secretion
• Cellular component: cytoplasm;extrinsic component of plasma membrane
• Molecular function: GTPase activity;ATP binding;ATPase activity