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. These statistics are base on transcript: . Only rare variants are included in the table.

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.

Effect	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
splice donor/acceptor (+/-2bp)		1				1
Total	2	1	107	68	13

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