LAT2

linker for activation of T cells family member 2

Basic information

Region (hg38): 7:74199652-74229834

Previous symbols: [ "WBSCR15", "WBSCR5" ]

Links

ENSG00000086730 ∙ NCBI:7462 ∙ OMIM:605719 ∙ HGNC:12749 ∙ Uniprot:Q9GZY6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LAT2 gene.

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.

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			17	6		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	6	0

Variants in LAT2

This is a list of pathogenic ClinVar variants found in the LAT2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
7-74216013-C-T		not specified	Uncertain significance (May 31, 2023)
7-74216055-G-A		not specified	Uncertain significance (Apr 17, 2023)
7-74216066-C-T		not specified	Uncertain significance (Dec 17, 2024)
7-74219746-G-A		not specified	Uncertain significance (Sep 09, 2024)
7-74219751-G-A		not specified	Likely benign (Nov 13, 2024)
7-74219767-C-T		not specified	Uncertain significance (Mar 29, 2023)
7-74219965-G-A		not specified	Likely benign (Jul 25, 2023)
7-74219980-G-C		not specified	Uncertain significance (Jun 17, 2024)
7-74219990-C-A		not specified	Likely benign (Mar 22, 2023)
7-74219990-C-T		not specified	Likely benign (Dec 17, 2021)
7-74220217-G-T		not specified	Uncertain significance (May 15, 2023)
7-74221651-T-C		not specified	Likely benign (May 29, 2024)
7-74221678-C-T		not specified	Uncertain significance (Nov 28, 2024)
7-74223726-G-A		not specified	Uncertain significance (Oct 29, 2024)
7-74223726-G-C		not specified	Uncertain significance (Jul 25, 2023)
7-74224036-T-C		not specified	Likely benign (Mar 06, 2023)
7-74224047-T-C		not specified	Uncertain significance (Jan 16, 2024)
7-74224099-G-A		not specified	Uncertain significance (May 31, 2023)
7-74224120-C-T		not specified	Uncertain significance (Dec 20, 2023)
7-74224171-A-G		not specified	Uncertain significance (Dec 17, 2024)
7-74224651-G-A		not specified	Uncertain significance (Feb 27, 2024)
7-74224657-C-T		not specified	Uncertain significance (Sep 25, 2024)
7-74224692-G-A		not specified	Uncertain significance (Jun 16, 2023)
7-74224695-G-A		not specified	Uncertain significance (Apr 15, 2024)
7-74224702-C-T		not specified	Uncertain significance (Aug 05, 2024)

GnomAD

Source: gnomAD

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: dbNSFP

• 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