NECTIN2

nectin cell adhesion molecule 2, the group of V-set domain containing|CD molecules|C2-set domain containing|Nectins and nectin-like molecules

Basic information

Region (hg38): 19:44846175-44889223

Previous symbols: [ "HVEB", "PVRL2" ]

Links

ENSG00000130202 ∙ NCBI:5819 ∙ OMIM:600798 ∙ HGNC:9707 ∙ Uniprot:Q92692 ∙ 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 NECTIN2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NECTIN2 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				14	3	17
missense			5	4	4	13
nonsense			1			1
start loss						0
frameshift						0
inframe indel				3		3
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding				1	1	2
Total	0	0	6	22	8

Variants in NECTIN2

This is a list of pathogenic ClinVar variants found in the NECTIN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-44865261-C-T		NECTIN2-related disorder	Likely benign (May 06, 2022)
19-44865306-G-A		not specified	Uncertain significance (Nov 15, 2021)
19-44865309-C-T		Cerebral palsy	Uncertain significance (Jun 10, 2021)
19-44865321-G-A		not specified	Uncertain significance (Oct 18, 2021)
19-44865329-C-T		NECTIN2-related disorder	Likely benign (Aug 10, 2019)
19-44865341-G-A		NECTIN2-related disorder	Likely benign (May 02, 2019)
19-44865470-G-A		NECTIN2-related disorder	Likely benign (Sep 17, 2019)
19-44865545-G-A		NECTIN2-related disorder	Likely benign (Sep 19, 2019)
19-44865548-C-T			Benign (May 31, 2018)
19-44865554-G-A		NECTIN2-related disorder	Likely benign (Jun 05, 2019)
19-44871836-TCTC-T		NECTIN2-related disorder	Likely benign (Apr 29, 2024)
19-44871890-G-A		NECTIN2-related disorder	Benign (Oct 28, 2019)
19-44871900-G-C		NECTIN2-related disorder	Benign (Jun 01, 2018)
19-44871907-C-T		NECTIN2-related disorder	Likely benign (Mar 10, 2023)
19-44872016-C-T		NECTIN2-related disorder	Likely benign (May 02, 2019)
19-44872038-C-T		NECTIN2-related disorder	Likely benign (May 06, 2022)
19-44873962-C-T		NECTIN2-related disorder	Likely benign (Jan 01, 2023)
19-44873997-G-A			Benign (May 30, 2018)
19-44874348-G-A		NECTIN2-related disorder	Likely benign (May 16, 2024)
19-44874354-C-T		NECTIN2-related disorder	Likely benign (Aug 14, 2019)
19-44878273-G-A			Benign (Mar 01, 2023)
19-44878275-G-T		NECTIN2-related disorder	Likely benign (Nov 01, 2019)
19-44878340-T-TGAG		NECTIN2-related disorder	Likely benign (Mar 26, 2023)
19-44878350-G-A		NECTIN2-related disorder	Likely benign (May 28, 2019)
19-44878362-T-TGGAGGAGCAGGA		NECTIN2-related disorder	Likely benign (Sep 01, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NECTIN2	protein_coding	protein_coding	ENST00000252483	9	43054

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.969	0.0307	124796	0	4	124800	0.0000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.64	241	324	0.743	0.0000199	3398
Missense in Polyphen		54	100.88	0.53531		1019
Synonymous	0.596	134	143	0.937	0.00000938	1182
Loss of Function	3.97	3	24.0	0.125	0.00000144	242

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000646	0.0000645
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000177	0.0000177
Middle Eastern	0.0000556	0.0000556
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Modulator of T-cell signaling. Can be either a costimulator of T-cell function, or a coinhibitor, depending on the receptor it binds to. Upon binding to CD226, stimulates T-cell proliferation and cytokine production, including that of IL2, IL5, IL10, IL13, and IFNG. Upon interaction with PVRIG, inhibits T-cell proliferation. These interactions are competitive (PubMed:26755705). Probable cell adhesion protein (PubMed:9657005). {ECO:0000269|PubMed:26755705, ECO:0000269|PubMed:9657005}.
• Pathway: Cell adhesion molecules (CAMs) - Homo sapiens (human);Adherens junction - Homo sapiens (human);Herpes simplex infection - Homo sapiens (human);Monoamine Transport;Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System;Cell-cell junction organization;Nectin/Necl trans heterodimerization;Adherens junctions interactions;Cell junction organization;Cell-Cell communication;Stabilization and expansion of the E-cadherin adherens junction;Nectin adhesion pathway (Consensus)

Recessive Scores

• pRec: 0.175

Intolerance Scores

• rvis_EVS: 0.56
• rvis_percentile_EVS: 81.63

Haploinsufficiency Scores

• pHI: 0.114
• hipred: Y
• hipred_score: 0.538
• ghis: 0.409

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Nectin2
• Phenotype: reproductive system phenotype; cellular phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: acrosome assembly;positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target;positive regulation of immunoglobulin mediated immune response;cytoskeleton organization;homophilic cell adhesion via plasma membrane adhesion molecules;spermatid development;spermatid nucleus differentiation;fertilization;fusion of virus membrane with host plasma membrane;sperm mitochondrion organization;cell part morphogenesis;positive regulation of mast cell activation;adherens junction organization;susceptibility to natural killer cell mediated cytotoxicity;adhesion of symbiont to host;cilium organization;positive regulation of natural killer cell mediated cytotoxicity;regulation of viral entry into host cell;coreceptor-mediated virion attachment to host cell;regulation of immune response;positive regulation of T cell receptor signaling pathway;establishment of mitochondrion localization;susceptibility to T cell mediated cytotoxicity
• Cellular component: plasma membrane;cell-cell junction;zonula adherens;focal adhesion;cell surface;integral component of membrane;cell-cell contact zone;extracellular exosome
• Molecular function: virus receptor activity;protein binding;coreceptor activity;identical protein binding;protein homodimerization activity;cell adhesion molecule binding