NLRP13

NLR family pyrin domain containing 13, the group of NLR family|Pyrin domain containing

Basic information

Region (hg38): 19:55891699-55932336

Previous symbols: [ "NALP13" ]

Links

ENSG00000173572 ∙ NCBI:126204 ∙ OMIM:609660 ∙ HGNC:22937 ∙ Uniprot:Q86W25 ∙ 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 NLRP13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NLRP13 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
missense			62	6	1	69
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	62	7	1

Variants in NLRP13

This is a list of pathogenic ClinVar variants found in the NLRP13 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-55895973-G-A			not provided (-)
19-55896034-G-T		not specified	Uncertain significance (Jul 14, 2022)
19-55896039-A-G		not specified	Uncertain significance (Jun 29, 2023)
19-55896048-A-G		not specified	Uncertain significance (Oct 16, 2024)
19-55896114-G-A		not specified	Uncertain significance (Nov 03, 2022)
19-55896115-C-G		not specified	Uncertain significance (Nov 09, 2024)
19-55896119-C-T		not specified	Likely benign (Feb 13, 2024)
19-55898792-G-A		not specified	Uncertain significance (Nov 14, 2024)
19-55898809-C-T		not specified	Uncertain significance (Jun 17, 2024)
19-55898825-C-T		not specified	Uncertain significance (Dec 09, 2023)
19-55898826-A-T		not specified	Uncertain significance (Oct 26, 2022)
19-55898872-T-C		not specified	Uncertain significance (Jul 27, 2024)
19-55898878-T-C		not specified	Uncertain significance (Dec 08, 2023)
19-55898905-C-T		not specified	Uncertain significance (Dec 10, 2024)
19-55898914-C-G		not specified	Uncertain significance (Feb 07, 2023)
19-55902139-C-G		not specified	Uncertain significance (Jul 30, 2024)
19-55902174-A-T			not provided (-)
19-55902177-C-T		not specified	Uncertain significance (Jan 06, 2023)
19-55902204-G-A		not specified	Uncertain significance (Nov 15, 2021)
19-55902212-G-T			not provided (-)
19-55902216-A-T			not provided (-)
19-55902229-T-C			not provided (-)
19-55902290-G-A			not provided (-)
19-55904951-T-A		not specified	Uncertain significance (Sep 05, 2024)
19-55905017-T-C		not specified	Uncertain significance (Dec 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NLRP13	protein_coding	protein_coding	ENST00000342929	11	40638

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.03e-16	0.627	122089	38	3621	125748	0.0147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.57	644	541	1.19	0.0000271	6905
Missense in Polyphen		166	142.16	1.1677		1962
Synonymous	-2.91	269	215	1.25	0.0000114	1942
Loss of Function	1.77	30	42.5	0.707	0.00000207	512

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00917	0.00917
Ashkenazi Jewish	0.00486	0.00487
East Asian	0.000762	0.000761
Finnish	0.0544	0.0541
European (Non-Finnish)	0.0175	0.0174
Middle Eastern	0.000762	0.000761
South Asian	0.00562	0.00554
Other	0.0114	0.0111

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in inflammation. {ECO:0000305}.

Recessive Scores

• pRec: 0.0803

Intolerance Scores

• loftool: 0.482
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.27

Haploinsufficiency Scores

• pHI: 0.0457
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0657

Gene Damage Prediction

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

Gene ontology

• Molecular function: ATP binding