NLRP7

NLR family pyrin domain containing 7, the group of Pyrin domain containing|NLR family

Basic information

Region (hg38): 19:54923509-54966312

Previous symbols: [ "NALP7" ]

Links

ENSG00000167634 ∙ NCBI:199713 ∙ OMIM:609661 ∙ HGNC:22947 ∙ Uniprot:Q8WX94 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complete hydatidiform mole (Supportive), mode of inheritance: AR
• hydatidiform mole, recurrent, 1 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Hydatidiform mole, recurrent, 1	AR	Obstetric; Oncologic	Women are likely to have pregnancies with hydatidiform moles, with a high risk of persistent trophoblastic disease, including requiring chemotherapeutic treatment, and awareness may allow reproductive planning and/or surveillance measures, which may allow early detection and treatment	Obstetric; Oncologic	16874523; 16462743; 19066229; 19246479; 22315435; 22770628; 23125094

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NLRP7 gene.

• Hydatidiform mole, recurrent, 1 (5 variants)
• Hydatidiform mole (2 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NLRP7 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			23	12	5	40
missense	4	1	89	10	4	108
nonsense	1					1
start loss						0
frameshift	2	2				4
inframe indel			1			1
splice donor/acceptor (+/-2bp)		1				1
splice region			1		1	2
non coding			9	3	3	15
Total	7	4	122	25	12

Highest pathogenic variant AF is 0.000230

Variants in NLRP7

This is a list of pathogenic ClinVar variants found in the NLRP7 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-54923557-C-T		Hydatidiform mole, recurrent, 1	Uncertain significance (Jan 13, 2018)
19-54923560-C-G		Hydatidiform mole, recurrent, 1	Likely benign (Jan 12, 2018)
19-54923696-C-T		Hydatidiform mole, recurrent, 1	Uncertain significance (Jan 13, 2018)
19-54923720-G-A		Hydatidiform mole, recurrent, 1	Uncertain significance (Jan 13, 2018)
19-54923735-G-A		Hydatidiform mole, recurrent, 1	Uncertain significance (Jan 13, 2018)
19-54923771-G-A		Hydatidiform mole, recurrent, 1 • Inborn genetic diseases	Uncertain significance (Oct 27, 2021)
19-54923772-T-C		Hydatidiform mole, recurrent, 1	Likely benign (Jan 13, 2018)
19-54923778-C-T		Hydatidiform mole, recurrent, 1	Uncertain significance (Jan 13, 2018)
19-54923785-A-G			Likely benign (Feb 01, 2023)
19-54923786-T-C		Hydatidiform mole, recurrent, 1	Uncertain significance (Jan 12, 2018)
19-54923823-C-G		Hydatidiform mole, recurrent, 1	Uncertain significance (Jan 13, 2018)
19-54923824-T-G		Inborn genetic diseases	Uncertain significance (Nov 08, 2022)
19-54923836-C-G		Inborn genetic diseases	Uncertain significance (Oct 25, 2023)
19-54923859-C-T		Inborn genetic diseases	Uncertain significance (Sep 01, 2021)
19-54923899-TC-T		Hydatidiform mole	Likely benign (Feb 22, 2021)
19-54927463-G-T		Hydatidiform mole, recurrent, 1	not provided (-)
19-54927482-A-G		Hydatidiform mole, recurrent, 1	not provided (-)
19-54927572-A-C		Hydatidiform mole, recurrent, 1	not provided (-)
19-54927572-AAAAC-A		Hydatidiform mole, recurrent, 1	not provided (-)
19-54927649-G-A			Likely benign (Jan 01, 2024)
19-54927695-A-G		Hydatidiform mole, recurrent, 1	not provided (-)
19-54927798-T-C		Hydatidiform mole	Benign (Feb 22, 2021)
19-54927800-C-G		Hydatidiform mole, recurrent, 1 • Hydatidiform mole	Benign (Feb 22, 2021)
19-54927803-G-A		Hydatidiform mole, recurrent, 1	not provided (-)
19-54927809-A-C		Hydatidiform mole, recurrent, 1	not provided (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NLRP7	protein_coding	protein_coding	ENST00000588756	10	42804

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.81e-16	0.312	125618	0	130	125748	0.000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.510	613	579	1.06	0.0000365	6811
Missense in Polyphen		138	134.81	1.0237		1813
Synonymous	-2.81	310	253	1.22	0.0000180	2018
Loss of Function	1.47	30	40.0	0.750	0.00000194	482

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00154	0.00117
Ashkenazi Jewish	0.000200	0.000198
East Asian	0.00131	0.00131
Finnish	0.00	0.00
European (Non-Finnish)	0.000444	0.000440
Middle Eastern	0.00131	0.00131
South Asian	0.000621	0.000621
Other	0.000979	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibits CASP1/caspase-1-dependent IL1B secretion. {ECO:0000269|PubMed:15817483}.
• Disease: DISEASE: Hydatidiform mole, recurrent, 1 (HYDM1) [MIM:231090]: A disorder characterized by excessive trophoblast development that produces a growing mass of tissue inside the uterus at the beginning of a pregnancy. It leads to abnormal pregnancies with no embryo, and cystic degeneration of the chorionic villi. {ECO:0000269|PubMed:16462743, ECO:0000269|PubMed:19246479}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: NOD-like receptor signaling pathway - Homo sapiens (human);Nucleotide-binding Oligomerization Domain (NOD) pathway (Consensus)

Recessive Scores

• pRec: 0.121

Intolerance Scores

• loftool: 0.900
• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.12

Haploinsufficiency Scores

• pHI: 0.0694
• hipred: N
• hipred_score: 0.139

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.108

Gene Damage Prediction

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

Gene ontology

• Biological process: negative regulation of endopeptidase activity;negative regulation of protein processing;negative regulation of interleukin-1 beta secretion;positive regulation of interleukin-1 beta secretion;cellular response to lipopolysaccharide;cellular response to interleukin-1;negative regulation of cytokine production involved in inflammatory response;negative regulation of aspartic-type peptidase activity
• Cellular component: cellular_component
• Molecular function: ATP binding;aspartic-type endopeptidase inhibitor activity;interleukin-1 binding;caspase binding