LIN9
Basic information
Region (hg38): 1:226231149-226309869
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (40 variants)
- not_provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the LIN9 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001366245.2. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 40 | 40 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 40 | 0 | 1 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| LIN9 | protein_coding | protein_coding | ENST00000328205 | 15 | 78721 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.998 | 0.00229 | 125735 | 0 | 3 | 125738 | 0.0000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.39 | 176 | 291 | 0.605 | 0.0000151 | 3659 |
| Missense in Polyphen | 29 | 87.448 | 0.33163 | 1068 | ||
| Synonymous | 0.462 | 93 | 98.8 | 0.941 | 0.00000490 | 1030 |
| Loss of Function | 4.89 | 4 | 35.4 | 0.113 | 0.00000198 | 420 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000295 | 0.0000295 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000896 | 0.00000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Acts as a tumor suppressor. Inhibits DNA synthesis. Its ability to inhibit oncogenic transformation is mediated through its association with RB1. Plays a role in the expression of genes required for the G1/S transition. {ECO:0000269|PubMed:15538385, ECO:0000269|PubMed:16730350}.;
- Pathway
- Cellular senescence - Homo sapiens (human);Gastric Cancer Network 1;Polo-like kinase mediated events;Transcription of E2F targets under negative control by DREAM complex;G0 and Early G1;Mitotic G1-G1/S phases;G2/M Transition;Mitotic G2-G2/M phases;Cell Cycle;Cell Cycle, Mitotic
(Consensus)
Recessive Scores
- pRec
- 0.421
Intolerance Scores
- loftool
- 0.102
- rvis_EVS
- -0.49
- rvis_percentile_EVS
- 22.36
Haploinsufficiency Scores
- pHI
- 0.534
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.576
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.239
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Lin9
- 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); reproductive system phenotype; embryo phenotype; immune system phenotype; digestive/alimentary 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); growth/size/body region phenotype; endocrine/exocrine gland phenotype; cellular phenotype;
Zebrafish Information Network
- Gene name
- lin9
- Affected structure
- olfactory system
- Phenotype tag
- abnormal
- Phenotype quality
- apoptotic
Gene ontology
- Biological process
- reproduction;transcription, DNA-templated;cell cycle;regulation of cell cycle;DNA biosynthetic process
- Cellular component
- nucleoplasm;transcriptional repressor complex
- Molecular function
- DNA binding;protein binding