NECTIN3

nectin cell adhesion molecule 3, the group of I-set domain containing|V-set domain containing|CD molecules|C2-set domain containing|Nectins and nectin-like molecules

Basic information

Region (hg38): 3:111070071-111275563

Previous symbols: [ "PVRL3" ]

Links

ENSG00000177707 ∙ NCBI:25945 ∙ OMIM:607147 ∙ HGNC:17664 ∙ Uniprot:Q9NQS3 ∙ 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 NECTIN3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NECTIN3 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				3	1	4
missense			4	1	3	8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1	5	6
Total	0	0	4	5	9

Variants in NECTIN3

This is a list of pathogenic ClinVar variants found in the NECTIN3 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-111072008-A-T		NECTIN3-related disorder	Likely benign (Jul 16, 2023)
3-111072032-G-A		NECTIN3-related disorder	Benign (Jun 10, 2021)
3-111072081-G-A		NECTIN3-related disorder	Benign (Dec 23, 2019)
3-111072090-C-G		NECTIN3-related disorder	Benign (Jan 20, 2020)
3-111072150-C-T		NECTIN3-related disorder	Benign (Nov 11, 2019)
3-111072155-G-A		NECTIN3-related disorder	Likely benign (May 28, 2019)
3-111072266-A-G			Benign (Jun 19, 2021)
3-111111899-ATGTGTG-A			Benign (Jun 19, 2021)
3-111111899-ATGTGTGTG-A			Benign (Jun 19, 2021)
3-111111899-ATGTGTGTGTG-A			Benign (Jun 20, 2021)
3-111112152-C-T		not specified	Uncertain significance (Nov 09, 2021)
3-111118754-G-A		not specified	Uncertain significance (Nov 09, 2021)
3-111118855-T-A		not specified	Uncertain significance (Jun 11, 2021)
3-111122207-A-C		Developmental cataract • NECTIN3-related disorder	Conflicting classifications of pathogenicity (Apr 16, 2024)
3-111125929-C-T			Benign (Jun 20, 2021)
3-111126223-C-T		NECTIN3-related disorder	Likely benign (Nov 13, 2019)
3-111133726-G-A		NECTIN3-related disorder	Likely benign (Jul 31, 2019)
3-111133790-G-A		NECTIN3-related disorder	Likely benign (Feb 03, 2023)
3-111133966-A-C			Likely benign (Nov 01, 2024)
3-111134210-G-A		not specified	Uncertain significance (Jul 27, 2021)
3-111145008-A-C		NECTIN3-related disorder	Benign (Nov 12, 2018)
3-111145130-G-A			Benign (Nov 12, 2018)
3-111147590-G-A			Benign (Nov 12, 2018)
3-111192236-AG-A			Benign (Nov 12, 2018)
3-111192402-C-A		NECTIN3-related disorder	Benign (Jul 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NECTIN3	protein_coding	protein_coding	ENST00000485303	6	205493

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.916	0.0843	125740	0	3	125743	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.770	245	281	0.871	0.0000136	3541
Missense in Polyphen		59	97.51	0.60506		1221
Synonymous	-1.43	123	104	1.18	0.00000534	1106
Loss of Function	3.66	3	21.2	0.142	0.00000106	281

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in cell-cell adhesion through heterophilic trans-interactions with nectin-like proteins or nectins, such as trans-interaction with NECTIN2 at Sertoli-spermatid junctions. Trans-interaction with PVR induces activation of CDC42 and RAC small G proteins through common signaling molecules such as SRC and RAP1. Also involved in the formation of cell-cell junctions, including adherens junctions and synapses. Induces endocytosis- mediated down-regulation of PVR from the cell surface, resulting in reduction of cell movement and proliferation. Plays a role in the morphology of the ciliary body. {ECO:0000269|PubMed:16216929}.
• Pathway: Cell adhesion molecules (CAMs) - Homo sapiens (human);Adherens junction - Homo sapiens (human);Cell-cell junction organization;Nectin/Necl trans heterodimerization;Adherens junctions interactions;Cell junction organization;Cell-Cell communication;Nectin adhesion pathway (Consensus)

Recessive Scores

• pRec: 0.186

Intolerance Scores

• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.45

Haploinsufficiency Scores

• pHI: 0.546
• hipred: Y
• hipred_score: 0.809
• ghis: 0.445

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Nectin3
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); vision/eye phenotype; skeleton phenotype; homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; craniofacial phenotype

Gene ontology

• Biological process: lens morphogenesis in camera-type eye;homophilic cell adhesion via plasma membrane adhesion molecules;heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules;spermatid development;fertilization;adherens junction organization;retina morphogenesis in camera-type eye;establishment of protein localization to plasma membrane;protein localization to cell junction
• Cellular component: plasma membrane;cell-cell junction;cell-cell adherens junction;apical junction complex;cell-cell contact zone;hippocampal mossy fiber to CA3 synapse;integral component of postsynaptic density membrane
• Molecular function: protein binding;signaling receptor activity;protein homodimerization activity;cell adhesion molecule binding