NLRP13

protein-coding

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

Gene summary

This gene encodes a member of the NACHT, leucine rich repeat, and PYD containing (NLRP) protein family. It has an N-terminal pyrin domain, followed by a NACHT domain, a NACHT-associated domain (NAD), and a C-terminal leucine-rich repeat (LRR) region. NLRP proteins are implicated in the activation of proinflammatory caspases through multiprotein complexes called inflammasomes. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Mar 2016]

Previous symbols:

NALP13

MANE transcript

NM_176810.2

Inheritance

—

ClinVar variants

U:161B:18

Top phenotype

Long QT syndrome

gnomAD constraint

pLI —, LoF o/e 0.71

Max pathogenic AF

—

Genomic locus

chr19:55,891,699-55,932,336

External References & Databases

Ensembl (ENSG00000173572)

Transcript & Mutation Effects

hg38 • Region Span ~40.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NLRP13 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 170

not providedTotal: 19

Long QT syndromeTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_176810.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				4 clinvar		4
missense			161 clinvar	13 clinvar	1 clinvar	175
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	161	17	1	179

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_176810.2	RefSeq	NP_789780.2	11	MANE Select
ENST00000342929.4	Ensembl	ENSP00000343891.3	11	MANE Select
NM_001321057.1	RefSeq	NP_001307986.1	12	Standard
ENST00000588751.5	Ensembl	ENSP00000467899.1	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

ATP binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000342929
Coding exons: 11
Length: 40638
Individuals with no LoFs: 122089
Homozygous LoFs: 38
Heterozygous LoFs: 3621
Defined: 125748
p: 0.0147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.57	644	541	1.19	0.0000271	6905
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0033	0.0033	notable
Latino/Admixed American	0.0058	0.0058	notable
Ashkenazi Jewish	0.0049	0.0049	notable
East Asian	0.00076	0.00076	rare
Finnish	0.054	0.054	notable
European (Non-Finnish)	0.018	0.017	notable
South Asian	0.0056	0.0055	notable
Other	0.011	0.011	notable

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0657

Gene Damage Prediction

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