NINJ1
Basic information
Region (hg38): 9:93121496-93134251
Links
Phenotypes
GenCC
Source:
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 NINJ1 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 | 0 | |||||
| missense | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 7 | 0 | 0 |
Variants in NINJ1
This is a list of pathogenic ClinVar variants found in the NINJ1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 9-93124916-G-C | not specified | Uncertain significance (Feb 10, 2022) | ||
| 9-93124957-G-T | not specified | Uncertain significance (Dec 01, 2022) | ||
| 9-93124976-C-T | not specified | Uncertain significance (Apr 26, 2024) | ||
| 9-93124979-C-T | not specified | Uncertain significance (Nov 08, 2021) | ||
| 9-93126419-T-C | not specified | Uncertain significance (Jun 18, 2021) | ||
| 9-93126434-C-T | not specified | Uncertain significance (Dec 05, 2024) | ||
| 9-93126437-C-T | not specified | Uncertain significance (Aug 26, 2024) | ||
| 9-93126491-C-T | not specified | Uncertain significance (Nov 07, 2022) | ||
| 9-93126554-T-C | not specified | Uncertain significance (Oct 06, 2021) | ||
| 9-93126637-G-A | not specified | Uncertain significance (Mar 18, 2024) | ||
| 9-93134210-G-A | not specified | Uncertain significance (Dec 28, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NINJ1 | protein_coding | protein_coding | ENST00000375446 | 3 | 12800 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.117 | 0.788 | 125727 | 0 | 7 | 125734 | 0.0000278 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.01 | 69 | 97.0 | 0.711 | 0.00000612 | 976 |
| Missense in Polyphen | 39 | 58.396 | 0.66785 | 577 | ||
| Synonymous | 0.391 | 45 | 48.5 | 0.929 | 0.00000384 | 313 |
| Loss of Function | 1.32 | 2 | 5.28 | 0.379 | 2.26e-7 | 58 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000906 | 0.0000904 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000353 | 0.0000352 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Homophilic cell adhesion molecule that promotes axonal growth. May play a role in nerve regeneration and in the formation and function of other tissues. Cell adhesion requires divalent cations.;
- Pathway
- Vitamin D Receptor Pathway
(Consensus)
Recessive Scores
- pRec
- 0.176
Intolerance Scores
- loftool
- 0.312
- rvis_EVS
- 0.35
- rvis_percentile_EVS
- 74.18
Haploinsufficiency Scores
- pHI
- 0.0953
- hipred
- N
- hipred_score
- 0.459
- ghis
- 0.433
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ninj1
- Phenotype
- cellular phenotype; growth/size/body region phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system 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); hematopoietic system phenotype; normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);
Gene ontology
- Biological process
- positive regulation of cell-matrix adhesion;cell adhesion;nervous system development;tissue regeneration;hyaloid vascular plexus regression
- Cellular component
- integral component of membrane
- Molecular function
- protein binding