NPTN
neuroplastin, the group of Basigin family |I-set domain containing
Basic information
Region (hg38): 15:73560013-73634134
Previous symbols: [ "SDFR1" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
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 | |||||
| missense | 9 | |||||
| nonsense | 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) | ||
| 15-73570204-C-A | not specified | Uncertain significance (Dec 21, 2022) | ||
| 15-73570221-G-A | not specified | Uncertain significance (Apr 23, 2024) | ||
| 15-73570236-A-G | not specified | Uncertain significance (Mar 07, 2024) | ||
| 15-73570265-C-T | Benign (Oct 09, 2018) | |||
| 15-73570327-C-T | not specified | Uncertain significance (Feb 07, 2023) | ||
| 15-73570333-G-A | not specified | Uncertain significance (Jun 13, 2024) | ||
| 15-73570341-G-A | not specified | Uncertain significance (Mar 01, 2023) | ||
| 15-73570346-C-A | not specified | Uncertain significance (Jan 23, 2024) | ||
| 15-73570426-G-A | Benign (Jun 29, 2018) | |||
| 15-73587575-C-T | not specified | Uncertain significance (Apr 27, 2022) | ||
| 15-73591997-T-G | not specified | Uncertain significance (Dec 20, 2023) | ||
| 15-73592077-G-A | not specified | Uncertain significance (Oct 04, 2022) | ||
| 15-73633152-G-A | not specified | Uncertain significance (Oct 17, 2023) | ||
| 15-73633202-G-T | Developmental disorder | Uncertain significance (Apr 09, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NPTN | protein_coding | protein_coding | ENST00000345330 | 8 | 74121 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.993 | 0.00696 | 115316 | 0 | 1 | 115317 | 0.00000434 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.68 | 126 | 244 | 0.517 | 0.0000148 | 2605 |
| Missense in Polyphen | 27 | 88.77 | 0.30416 | 936 | ||
| Synonymous | 1.30 | 81 | 97.4 | 0.832 | 0.00000653 | 794 |
| Loss of Function | 3.85 | 1 | 19.2 | 0.0520 | 9.51e-7 | 218 |
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 | 0.0000468 | 0.0000468 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
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