NPIPB7
protein-codingnuclear pore complex interacting protein family member B7
Gene summary
Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Jul 2025]
- NPIPL1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~16.0 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 NPIPB7 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001396030.1. 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 | 3 | 3 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 0 | 4 | 0 | 4 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001382959.1 | 7 | MANE Select | |
| Ensembl | ENSP00000405348.1 | 7 | MANE Select | |
| Ensembl | ENSP00000415207.4 | 7 | Standard | |
| Ensembl | ENSP00000499219.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Cellular Component
- extracellular region
- nucleoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000452313
- Coding exons
- 7
- Length
- 14176
- Individuals with no LoFs
- 108155
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 12
- Defined
- 108167
- p
- 0.0000555
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.349 | 52 | 45.4 | 1.15 | 0.00000248 | 2609 |
| Missense (PolyPhen) | 22 | 18.732 | 1.1745 | 1095 | ||
| Synonymous | 0.268 | 16 | 17.4 | 0.918 | 9.41e-7 | 821 |
| Loss of Function | -0.572 | 2 | 1.30 | 1.54 | 5.52e-8 | 128 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.00028 | 0.00028 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000010 | 0.000010 | rare |
| South Asian | 0.000076 | 0.000076 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |