NPTN

neuroplastin, the group of Basigin family |I-set domain containing

Basic information

Region (hg38): 15:73560014-73634134

Previous symbols: [ "SDFR1" ]

Links

ENSG00000156642NCBI:27020OMIM:612820HGNC:17867Uniprot:Q9Y639AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NPTN 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
1
clinvar
1
missense
9
clinvar
9
nonsense
1
clinvar
1
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
1
1
non coding
0
Total 0 0 10 0 1

Variants in NPTN

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

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

Position Type Phenotype Significance ClinVar
15-73563248-G-A not specified Uncertain significance (Apr 29, 2024)3300856
15-73570204-C-A not specified Uncertain significance (Dec 21, 2022)2338786
15-73570221-G-A not specified Uncertain significance (Apr 23, 2024)3300855
15-73570236-A-G not specified Uncertain significance (Mar 07, 2024)3201783
15-73570265-C-T Benign (Oct 09, 2018)791101
15-73570327-C-T not specified Uncertain significance (Feb 07, 2023)2480674
15-73570333-G-A not specified Uncertain significance (Jun 13, 2024)3300854
15-73570341-G-A not specified Uncertain significance (Mar 01, 2023)2461135
15-73570346-C-A not specified Uncertain significance (Jan 23, 2024)3201786
15-73570426-G-A Benign (Jun 29, 2018)779895
15-73587575-C-T not specified Uncertain significance (Apr 27, 2022)2389380
15-73591997-T-G not specified Uncertain significance (Dec 20, 2023)2295702
15-73592077-G-A not specified Uncertain significance (Oct 04, 2022)2316451
15-73633152-G-A not specified Uncertain significance (Oct 17, 2023)3201784
15-73633202-G-T Developmental disorder Uncertain significance (Apr 09, 2021)1343197

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
NPTNprotein_codingprotein_codingENST00000345330 874121
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9930.00696115316011153170.00000434
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.681262440.5170.00001482605
Missense in Polyphen2788.770.30416936
Synonymous1.308197.40.8320.00000653794
Loss of Function3.85119.20.05209.51e-7218

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.00004680.0000468
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Probable homophilic and heterophilic cell adhesion molecule involved in long term potentiation at hippocampal excitatory synapses through activation of p38MAPK. May also regulate neurite outgrowth by activating the FGFR1 signaling pathway. May play a role in synaptic plasticity (By similarity). {ECO:0000250}.;
Pathway
Neuronal System;Neurotransmitter receptors and postsynaptic signal transmission;Transmission across Chemical Synapses (Consensus)

Recessive Scores

pRec
0.149

Intolerance Scores

loftool
rvis_EVS
-0.45
rvis_percentile_EVS
24

Haploinsufficiency Scores

pHI
0.258
hipred
Y
hipred_score
0.550
ghis
0.619

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.874

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Nptn
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); hearing/vestibular/ear phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); growth/size/body region phenotype; hematopoietic system phenotype; homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan);

Gene ontology

Biological process
positive regulation of protein phosphorylation;homophilic cell adhesion via plasma membrane adhesion molecules;positive regulation of cytosolic calcium ion concentration;axon guidance;visual learning;positive regulation of neuron projection development;positive regulation of fibroblast growth factor receptor signaling pathway;positive regulation of long-term neuronal synaptic plasticity;long-term synaptic potentiation;positive regulation of ERK1 and ERK2 cascade;dendrite self-avoidance;trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission;positive regulation of long-term synaptic potentiation;regulation of receptor localization to synapse;positive regulation of cellular protein localization;excitatory synapse assembly
Cellular component
plasma membrane;cell surface;axon;dendrite;presynaptic membrane;inhibitory synapse;Schaffer collateral - CA1 synapse;glutamatergic synapse;GABA-ergic synapse;integral component of presynaptic active zone membrane;integral component of postsynaptic density membrane
Molecular function
type 1 fibroblast growth factor receptor binding;ion channel binding;cell adhesion molecule binding;cell-cell adhesion mediator activity