NIPSNAP3A
protein-codingnipsnap homolog 3A
Gene summary
NIPSNAP3A belongs to a family of proteins with putative roles in vesicular transport (Buechler et al., 2004 [PubMed 15177564]).[supplied by OMIM, Mar 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~12.4 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 NIPSNAP3A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_015469.3. 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 | 4 | 4 | ||||
| missense | 37 | 37 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 0 | 45 | 0 | 0 | 45 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_056284.1 | 6 | MANE Select | |
| Ensembl | ENSP00000363899.4 | 6 | MANE Select | |
| RefSeq | NP_001316499.1 | 5 | Standard | |
| Ensembl | ENSP00000557971.1 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Molecular Function
- protein binding
Cellular Component
- nucleus
- mitochondrion
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000374767
- Coding exons
- 6
- Length
- 12435
- Individuals with no LoFs
- 124947
- Homozygous LoFs
- 6
- Heterozygous LoFs
- 795
- Defined
- 125748
- p
- 0.00319
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.295 | 144 | 134 | 1.07 | 0.00000689 | 1599 |
| Missense (PolyPhen) | 49 | 40.848 | 1.1996 | 493 | ||
| Synonymous | -0.474 | 54 | 49.7 | 1.09 | 0.00000265 | 479 |
| Loss of Function | -0.828 | 16 | 12.8 | 1.25 | 5.45e-7 | 156 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.027 | 0.027 | notable |
| Latino/Admixed American | 0.0027 | 0.0026 | notable |
| Ashkenazi Jewish | 0.0057 | 0.0057 | notable |
| East Asian | 0.00049 | 0.00049 | rare |
| Finnish | 0.00037 | 0.00037 | rare |
| European (Non-Finnish) | 0.0016 | 0.0016 | notable |
| South Asian | 0.00033 | 0.00029 | rare |
| Other | 0.0018 | 0.0018 | notable |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.0977
Intolerance Scores
- LoFtool
- 0.686
- RVIS EVS
- -0.07
- RVIS percentile EVS
- 48.35
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.801
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |