LRRTM2
Basic information
Region (hg38): 5:138868921-138875368
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (38 variants)
- not_provided (1 variants)
- Hereditary_cancer-predisposing_syndrome (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRTM2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015564.3. 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 | 37 | 38 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 37 | 2 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| LRRTM2 | protein_coding | protein_coding | ENST00000274711 | 2 | 6446 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.809 | 0.191 | 124633 | 0 | 4 | 124637 | 0.0000160 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.89 | 190 | 279 | 0.682 | 0.0000152 | 3387 |
| Missense in Polyphen | 55 | 112.31 | 0.48969 | 1428 | ||
| Synonymous | 0.942 | 97 | 110 | 0.886 | 0.00000598 | 1022 |
| Loss of Function | 3.36 | 3 | 18.6 | 0.161 | 0.00000115 | 213 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000556 | 0.0000556 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000266 | 0.0000265 |
| Middle Eastern | 0.0000556 | 0.0000556 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in the development and maintenance of excitatory synapse in the vertebrate nervous system. Regulates surface expression of AMPA receptors and instructs the development of functional glutamate release sites. Acts as a ligand for the presynaptic receptors NRXN1-A and NRXN1-B (By similarity). {ECO:0000250}.;
- Pathway
- Neuronal System;Neurexins and neuroligins;Protein-protein interactions at synapses
(Consensus)
Recessive Scores
- pRec
- 0.118
Intolerance Scores
- loftool
- 0.246
- rvis_EVS
- -0.6
- rvis_percentile_EVS
- 17.75
Haploinsufficiency Scores
- pHI
- 0.817
- hipred
- Y
- hipred_score
- 0.768
- ghis
- 0.416
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.394
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Lrrtm2
- 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);
Gene ontology
- Biological process
- negative regulation of receptor internalization;synapse organization;positive regulation of synapse assembly;long-term synaptic potentiation;regulation of postsynaptic density assembly
- Cellular component
- cell junction;excitatory synapse;Schaffer collateral - CA1 synapse;hippocampal mossy fiber to CA3 synapse;glutamatergic synapse;GABA-ergic synapse;integral component of postsynaptic specialization membrane;integral component of postsynaptic density membrane
- Molecular function
- neurexin family protein binding