LAT2
Basic information
Region (hg38): 7:74199652-74229834
Previous symbols: [ "WBSCR15", "WBSCR5" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (35 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the LAT2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000032464.3. 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 | 0 | |||||
| missense | 28 | 35 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 28 | 7 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| LAT2 | protein_coding | protein_coding | ENST00000460943 | 11 | 30180 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000223 | 0.982 | 124770 | 2 | 26 | 124798 | 0.000112 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.0248 | 145 | 144 | 1.01 | 0.00000835 | 1553 |
| Missense in Polyphen | 41 | 44.397 | 0.92348 | 519 | ||
| Synonymous | 1.39 | 47 | 60.8 | 0.774 | 0.00000398 | 459 |
| Loss of Function | 2.09 | 9 | 18.8 | 0.479 | 7.99e-7 | 220 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000740 | 0.0000646 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000190 | 0.000177 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000203 | 0.000163 |
| Other | 0.000343 | 0.000330 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in FCER1 (high affinity immunoglobulin epsilon receptor)-mediated signaling in mast cells. May also be involved in BCR (B-cell antigen receptor)-mediated signaling in B-cells and FCGR1 (high affinity immunoglobulin gamma Fc receptor I)-mediated signaling in myeloid cells. Couples activation of these receptors and their associated kinases with distal intracellular events through the recruitment of GRB2. {ECO:0000269|PubMed:12486104, ECO:0000269|PubMed:12514734, ECO:0000269|PubMed:15010370}.;
- Disease
- DISEASE: Note=LAT2 is located in the Williams-Beuren syndrome (WBS) critical region. WBS results from a hemizygous deletion of several genes on chromosome 7q11.23, thought to arise as a consequence of unequal crossing over between highly homologous low-copy repeat sequences flanking the deleted region. Haploinsufficiency of LAT2 may be the cause of certain cardiovascular and musculo-skeletal abnormalities observed in the disease. {ECO:0000269|PubMed:11003705, ECO:0000269|PubMed:11124535, ECO:0000269|Ref.5}.;
- Pathway
- B Cell Receptor Signaling Pathway;Fc epsilon receptor (FCERI) signaling;Innate Immune System;Immune System;BCR;Fc-epsilon receptor I signaling in mast cells;Role of LAT2/NTAL/LAB on calcium mobilization
(Consensus)
Recessive Scores
- pRec
- 0.0928
Intolerance Scores
- loftool
- 0.629
- rvis_EVS
- 0.08
- rvis_percentile_EVS
- 60.09
Haploinsufficiency Scores
- pHI
- 0.103
- hipred
- Y
- hipred_score
- 0.511
- ghis
- 0.526
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.517
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Lat2
- Phenotype
- homeostasis/metabolism phenotype; immune system 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); hematopoietic system phenotype;
Gene ontology
- Biological process
- adaptive immune response;calcium-mediated signaling;intracellular signal transduction;Fc-epsilon receptor signaling pathway;B cell activation;mast cell degranulation;B cell receptor signaling pathway
- Cellular component
- plasma membrane;integral component of membrane;mast cell granule;membrane raft;extracellular exosome
- Molecular function
- protein binding;SH2 domain binding