NLRP5

NLR family pyrin domain containing 5, the group of Subcortical maternal complex|NLR family|Pyrin domain containing

Basic information

Region (hg38): 19:55999726-56061810

Previous symbols: [ "NALP5" ]

Links

ENSG00000171487 ∙ NCBI:126206 ∙ OMIM:609658 ∙ HGNC:21269 ∙ Uniprot:P59047 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• oocyte/zygote/embryo maturation arrest 19 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Oocyte/zygote/embryo maturation arrest 19	AR	General	Some individuals have been described as able to achieve successful pregnancies using IVF	Obstetric	30877238; 32222962; 35091966; 35946397

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NLRP5 gene.

• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NLRP5 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				33	9	42
missense			106	35	4	145
nonsense	1					1
start loss						0
frameshift	1		1			2
inframe indel						0
splice donor/acceptor (+/-2bp)		1				1
splice region			1	1	1	3
non coding						0
Total	2	1	107	68	13

Variants in NLRP5

This is a list of pathogenic ClinVar variants found in the NLRP5 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-55999779-A-C			Likely benign (May 25, 2018)
19-55999787-C-T			Uncertain significance (Feb 01, 2023)
19-55999788-G-A			Likely pathogenic (Jul 05, 2022)
19-56003724-C-T		not specified	Uncertain significance (Dec 27, 2023)
19-56003730-C-T		not specified	Uncertain significance (Nov 09, 2024)
19-56003772-T-C		not specified	Uncertain significance (Jul 14, 2022)
19-56003823-C-T		not specified	Likely benign (Oct 04, 2024)
19-56003843-G-A		not specified	Uncertain significance (Jan 03, 2024)
19-56003843-G-T		not specified	Uncertain significance (Nov 02, 2023)
19-56003854-G-T		not specified	Uncertain significance (Mar 27, 2023)
19-56003902-A-T		not specified	Uncertain significance (Nov 11, 2024)
19-56003945-C-T		Oocyte/zygote/embryo maturation arrest 19	Pathogenic (May 02, 2023)
19-56003946-A-G		not specified	Uncertain significance (Oct 03, 2022)
19-56003953-A-C		not specified	Uncertain significance (Jul 14, 2021)
19-56003956-C-T			Likely benign (Oct 10, 2018)
19-56003958-A-G		not specified	Uncertain significance (Dec 14, 2023)
19-56003965-C-T		NLRP5-related disorder	Benign (Mar 06, 2024)
19-56003968-C-T		NLRP5-related disorder	Benign (Jan 05, 2024)
19-56003969-G-A		not specified	Uncertain significance (Oct 25, 2023)
19-56003993-C-A		not specified	Uncertain significance (Apr 14, 2022)
19-56004028-G-A			Likely benign (Jan 09, 2018)
19-56004060-G-A			Likely benign (Jun 26, 2020)
19-56004072-A-G		NLRP5-related disorder	Likely benign (Dec 31, 2019)
19-56004091-G-T		not specified	Uncertain significance (Dec 16, 2023)
19-56004101-C-T			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NLRP5	protein_coding	protein_coding	ENST00000390649	15	62088

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.14e-13	0.995	124515	0	164	124679	0.000658

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.21	863	698	1.24	0.0000419	7801
Missense in Polyphen		170	156.76	1.0845		2141
Synonymous	-3.90	381	296	1.29	0.0000194	2395
Loss of Function	2.73	29	49.8	0.583	0.00000253	577

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00102	0.00102
Ashkenazi Jewish	0.00119	0.00119
East Asian	0.000557	0.000556
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.000771	0.000770
Middle Eastern	0.000557	0.000556
South Asian	0.000753	0.000752
Other	0.00117	0.00116

dbNSFP

Source: dbNSFP

• Function: FUNCTION: As a member of the subcortical maternal complex (SCMC), plays an essential role for zygotes to progress beyond the first embryonic cell divisions. {ECO:0000250}.
• Pathway: Preimplantation Embryo (Consensus)

Intolerance Scores

• loftool: 0.504
• rvis_EVS: 0.18
• rvis_percentile_EVS: 66.14

Haploinsufficiency Scores

• pHI: 0.0600
• hipred: N
• hipred_score: 0.251

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.109

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nlrp5
• Phenotype: embryo phenotype; reproductive system phenotype

Gene ontology

• Cellular component: nucleolus;mitochondrion
• Molecular function: ATP binding