LAX1

lymphocyte transmembrane adaptor 1

Basic information

Region (hg38): 1:203765177-203778175

Links

ENSG00000122188 ∙ NCBI:54900 ∙ OMIM:619622 ∙ HGNC:26005 ∙ Uniprot:Q8IWV1 ∙ 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 LAX1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LAX1 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				2	2	4
missense			13	3		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	5	2

Variants in LAX1

This is a list of pathogenic ClinVar variants found in the LAX1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-203765593-A-G		not specified	Uncertain significance (Jun 19, 2024)
1-203765607-G-T		not specified	Uncertain significance (Apr 01, 2024)
1-203765641-C-G		not specified	Likely benign (Jul 19, 2022)
1-203765646-C-A		not specified	Uncertain significance (Jun 22, 2023)
1-203770866-C-T		not specified	Uncertain significance (May 08, 2024)
1-203770877-G-A		not specified	Uncertain significance (Aug 04, 2021)
1-203771380-C-T			Benign (Mar 30, 2018)
1-203771422-C-A			Benign (Mar 30, 2018)
1-203772083-G-C		not specified	Uncertain significance (Apr 05, 2023)
1-203773922-T-A		not specified	Uncertain significance (Nov 10, 2022)
1-203773936-C-T		not specified	Uncertain significance (Aug 04, 2023)
1-203773976-T-G		not specified	Uncertain significance (Feb 27, 2024)
1-203774031-G-T		not specified	Uncertain significance (Jul 14, 2022)
1-203774035-G-A		not specified	Uncertain significance (Feb 06, 2023)
1-203774045-A-G			Likely benign (May 01, 2022)
1-203774149-C-T		not specified	Uncertain significance (Nov 10, 2022)
1-203774158-T-C		not specified	Uncertain significance (Aug 09, 2021)
1-203774288-T-C			Likely benign (May 01, 2022)
1-203774296-T-C		not specified	Uncertain significance (Feb 27, 2024)
1-203774332-A-G		not specified	Uncertain significance (Jul 12, 2022)
1-203774418-G-A			Likely benign (Mar 30, 2018)
1-203774448-G-A		not specified	Uncertain significance (Aug 10, 2021)
1-203774578-T-C		not specified	Likely benign (Sep 09, 2021)
1-203774637-G-A		not specified	Uncertain significance (Mar 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LAX1	protein_coding	protein_coding	ENST00000442561	5	11058

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000296	0.813	125705	0	40	125745	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.432	202	220	0.918	0.0000114	2630
Missense in Polyphen		54	62.596	0.86267		804
Synonymous	0.0983	86	87.2	0.987	0.00000513	763
Loss of Function	1.17	7	11.2	0.623	8.35e-7	89

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000329	0.000329
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000323	0.000323
European (Non-Finnish)	0.000185	0.000185
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Negatively regulates TCR (T-cell antigen receptor)- mediated signaling in T-cells and BCR (B-cell antigen receptor)- mediated signaling in B-cells. {ECO:0000269|PubMed:12359715}.
• Pathway: TCR (Consensus)

Recessive Scores

• pRec: 0.282

Intolerance Scores

• loftool: 0.127
• rvis_EVS: 1.24
• rvis_percentile_EVS: 93.39

Haploinsufficiency Scores

• pHI: 0.103
• hipred: N
• hipred_score: 0.352
• ghis: 0.400

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.392

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Lax1
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: inactivation of MAPK activity;adaptive immune response;immune response;intracellular signal transduction;B cell activation;negative regulation of T cell activation
• Cellular component: Golgi apparatus;cytosol;plasma membrane;membrane;integral component of membrane;membrane raft
• Molecular function: protein binding;protein kinase binding;SH2 domain binding