NPTN
protein-codingneuroplastin, the group of Basigin family |I-set domain containing
Gene summary
This gene encodes a type I transmembrane protein belonging to the Ig superfamily. The protein is believed to be involved in cell-cell interactions or cell-substrate interactions. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2009]
- SDFR1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~74.1 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to NPTN variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_012428.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 2 | 29 | 31 | |||
| nonsense | 1 | 3 | 1 | 5 | ||
| start loss | 0 | |||||
| frameshift | 1 | 1 | 2 | |||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 2 | 6 | 34 | 0 | 1 | 43 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_036560.1 | 8 | MANE Select | |
| Ensembl | ENSP00000290401.4 | 8 | MANE Select | |
| RefSeq | NP_001154835.1 | 8 | Standard | |
| RefSeq | NP_001154836.1 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Neuronal System
- Neurotransmitter receptors and postsynaptic signal transmission
- Transmission across Chemical Synapses
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
Molecular Function
- type 1 fibroblast growth factor receptor binding
- ion channel binding
- cell adhesion molecule binding
- cell-cell adhesion mediator activity
Cellular Component
- plasma membrane
- cell surface
- axon
- dendrite
- presynaptic membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000345330
- Coding exons
- 8
- Length
- 74121
- Individuals with no LoFs
- 115316
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 1
- Defined
- 115317
- p
- 0.00000434
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.68 | 126 | 244 | 0.517 | 0.0000148 | 2605 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000047 | 0.000047 | rare |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
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}.;
Recessive Scores
- pRec
- 0.149
Intolerance Scores
- RVIS EVS
- -0.45
- RVIS percentile EVS
- 24
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.874
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |