NRP2

neuropilin 2

Basic information

Region (hg38): 2:205681989-205798133

Links

ENSG00000118257 ∙ NCBI:8828 ∙ OMIM:602070 ∙ HGNC:8005 ∙ Uniprot:O60462 ∙ 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 NRP2 gene.

• NRP2-related condition (30 variants)
• not provided (29 variants)
• Inborn genetic diseases (29 variants)
• not specified (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NRP2 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				11	6	17
missense			54	7	3	64
nonsense					1	1
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	2	3
non coding				1		1
Total	0	1	54	19	10

Highest pathogenic variant AF is 0.00000657

Variants in NRP2

This is a list of pathogenic ClinVar variants found in the NRP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-205683331-A-G		not specified	Uncertain significance (May 31, 2023)
2-205683331-A-T		not specified	Uncertain significance (Feb 28, 2023)
2-205683345-C-G		NRP2-related disorder • not specified	Conflicting classifications of pathogenicity (Dec 12, 2023)
2-205697551-G-A		NRP2-related disorder	Likely benign (Apr 21, 2022)
2-205697555-G-A		NRP2-related disorder	Uncertain significance (Sep 13, 2023)
2-205697562-G-A		not specified	Uncertain significance (Dec 13, 2023)
2-205697593-C-T		NRP2-related disorder	Benign (Nov 22, 2022)
2-205697599-C-T		NRP2-related disorder	Likely benign (Aug 31, 2021)
2-205697620-C-G		NRP2-related disorder	Likely benign (Dec 23, 2021)
2-205697636-G-A		not specified	Uncertain significance (Jan 23, 2024)
2-205697638-G-A		NRP2-related disorder	Likely benign (Jan 28, 2022)
2-205697650-C-T		NRP2-related disorder	Likely benign (Jun 16, 2023)
2-205697656-C-T		NRP2-related disorder	Likely benign (Jun 08, 2022)
2-205697657-G-A		not specified	Uncertain significance (Jan 18, 2022)
2-205697661-C-T		not specified	Uncertain significance (Aug 14, 2023)
2-205697704-C-T		NRP2-related disorder	Likely benign (Feb 03, 2023)
2-205697730-C-T		NRP2-related disorder	Likely benign (Jul 13, 2021)
2-205697731-G-A		NRP2-related disorder	Likely benign (Jan 05, 2024)
2-205716203-A-G		not specified	Uncertain significance (Dec 12, 2023)
2-205716245-G-A		not specified	Uncertain significance (Feb 15, 2023)
2-205716278-A-G		not specified	Uncertain significance (Jan 16, 2024)
2-205716295-C-T		NRP2-related disorder	Likely benign (Nov 08, 2022)
2-205716309-A-G		not specified	Benign (May 04, 2022)
2-205716328-C-A		NRP2-related disorder	Benign/Likely benign (Oct 27, 2021)
2-205716359-G-C		not specified	Uncertain significance (Jun 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NRP2	protein_coding	protein_coding	ENST00000360409	17	116144

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000807	0.999	125708	0	40	125748	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.18	472	550	0.858	0.0000347	6126
Missense in Polyphen		199	273.56	0.72744		3035
Synonymous	-0.510	236	226	1.04	0.0000157	1806
Loss of Function	4.47	15	48.6	0.308	0.00000242	525

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000515	0.000514
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000176	0.000176
Middle Eastern	0.000326	0.000326
South Asian	0.0000653	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: High affinity receptor for semaphorins 3C, 3F, VEGF-165 and VEGF-145 isoforms of VEGF, and the PLGF-2 isoform of PGF.
• Pathway: VEGFA-VEGFR2 Signaling Pathway;EMT transition in Colorectal Cancer;Developmental Biology;Signal Transduction;Neurophilin interactions with VEGF and VEGFR;NrCAM interactions;Signaling by VEGF;L1CAM interactions;Axon guidance;Signaling by Receptor Tyrosine Kinases;VEGF and VEGFR signaling network;VEGFR1 specific signals (Consensus)

Recessive Scores

• pRec: 0.151

Intolerance Scores

• loftool: 0.0247
• rvis_EVS: -1.08
• rvis_percentile_EVS: 7.28

Haploinsufficiency Scores

• pHI: 0.310
• hipred: Y
• hipred_score: 0.744
• ghis: 0.550

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.986

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nrp2
• 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; cellular phenotype; homeostasis/metabolism phenotype; craniofacial phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); muscle 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); reproductive system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; embryo phenotype; immune system phenotype

Zebrafish Information Network

• Gene name: nrp2b
• Affected structure: cranial neural crest
• Phenotype tag: abnormal
• Phenotype quality: disrupted

Gene ontology

• Biological process: angiogenesis;positive regulation of endothelial cell proliferation;outflow tract septum morphogenesis;cell adhesion;axon guidance;positive regulation of endothelial cell migration;viral process;facial nerve structural organization;vestibulocochlear nerve structural organization;nerve development;gonadotrophin-releasing hormone neuronal migration to the hypothalamus;ventral trunk neural crest cell migration;vascular endothelial growth factor signaling pathway;vascular endothelial growth factor receptor signaling pathway;axon extension involved in axon guidance;negative chemotaxis;sympathetic ganglion development;trigeminal ganglion development;sensory neuron axon guidance;sympathetic neuron projection extension;sympathetic neuron projection guidance;regulation of postsynapse organization;neural crest cell migration involved in autonomic nervous system development;semaphorin-plexin signaling pathway involved in neuron projection guidance;facioacoustic ganglion development;dorsal root ganglion morphogenesis;cellular response to leukemia inhibitory factor
• Cellular component: semaphorin receptor complex;extracellular region;plasma membrane;membrane;integral component of membrane;axon;glutamatergic synapse;integral component of postsynaptic membrane
• Molecular function: vascular endothelial growth factor-activated receptor activity;protein binding;heparin binding;semaphorin receptor activity;growth factor binding;cytokine binding;signaling receptor activity;metal ion binding