NEPRO
Genenucleolus and neural progenitor protein
Gene summary
No gene description available in the current model. Review primary literature for detailed gene function and characteristics.
- C3orf17
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
GenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
Clinical Genomic Database (CGD)
Manifestation: Craniofacial; Musculoskeletal; Neurologic
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to NEPRO variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript . 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 | 2 | |||
| missense | 1 | 5 | 1 | 2 | 9 | |
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 1 | 0 | 6 | 2 | 3 | 12 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| No transcripts match your selected source or search query. | ||||
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- negative regulation of neuron differentiation
- positive regulation of Notch signaling pathway
Cellular Component
- nucleus
- nucleolus
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000314400
- Coding exons
- 9
- Length
- 17422
- Individuals with no LoFs
- 125574
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 174
- Defined
- 125748
- p
- 0.000692
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.0895 | 299 | 295 | 1.01 | 0.0000144 | 3728 |
| Missense (PolyPhen) | 85 | 92.646 | 0.91747 | 1219 | ||
| Synonymous | 1.17 | 91 | 106 | 0.856 | 0.00000519 | 1046 |
| Loss of Function | 1.68 | 16 | 25.1 | 0.638 | 0.00000114 | 340 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0024 | 0.0023 | notable |
| Latino/Admixed American | 0.00038 | 0.00038 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.0014 | 0.0014 | notable |
| Finnish | 0.00084 | 0.00083 | rare |
| European (Non-Finnish) | 0.00057 | 0.00055 | rare |
| South Asian | 0.00038 | 0.00036 | rare |
| Other | 0.00083 | 0.00081 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May play a role in cortex development as part of the Notch signaling pathway. Downstream of Notch may repress the expression of proneural genes and inhibit neuronal differentiation thereby maintaining neural progenitors. May also play a role in preimplentation embryo development. {ECO:0000250|UniProtKB:Q8R2U2}.;
Recessive Scores
- pRec
- 0.0708
Intolerance Scores
- RVIS EVS
- 0.73
- RVIS percentile EVS
- 86.3
Essentials
- Essential (gene trap)
- E