LIME1

Lck interacting transmembrane adaptor 1

Basic information

Region (hg38): 20:63736283-63739103

Links

ENSG00000203896 ∙ NCBI:54923 ∙ OMIM:609809 ∙ HGNC:26016 ∙ Uniprot:Q9H400 ∙ 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 LIME1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LIME1 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			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	0

Variants in LIME1

This is a list of pathogenic ClinVar variants found in the LIME1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-63737559-C-T		not specified	Uncertain significance (Aug 13, 2021)
20-63737625-G-A		not specified	Uncertain significance (Jan 23, 2024)
20-63737825-G-A		not specified	Uncertain significance (Dec 06, 2022)
20-63737828-G-A		not specified	Uncertain significance (Oct 06, 2021)
20-63737855-C-T		not specified	Uncertain significance (Dec 17, 2023)
20-63737862-A-G		not specified	Uncertain significance (Dec 14, 2023)
20-63737877-A-C		not specified	Uncertain significance (Jan 09, 2024)
20-63737886-C-A		not specified	Uncertain significance (Apr 07, 2022)
20-63737891-G-A		not specified	Uncertain significance (Jul 13, 2021)
20-63737898-A-C		not specified	Uncertain significance (Sep 25, 2023)
20-63737994-C-T		not specified	Uncertain significance (May 30, 2024)
20-63738054-A-G		not specified	Uncertain significance (Nov 09, 2022)
20-63738194-G-A		not specified	Uncertain significance (May 17, 2023)
20-63738267-C-G		not specified	Uncertain significance (Mar 21, 2023)
20-63738330-C-T		not specified	Uncertain significance (Aug 10, 2021)
20-63738399-C-T		not specified	Uncertain significance (Jun 09, 2022)
20-63738422-G-A		not specified	Likely benign (Mar 07, 2025)
20-63738434-A-C		not specified	Uncertain significance (May 05, 2023)
20-63738675-G-C		not specified	Uncertain significance (Jan 22, 2025)
20-63738812-G-A		not specified	Uncertain significance (Aug 16, 2022)
20-63738868-G-A		not specified	Uncertain significance (Aug 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LIME1	protein_coding	protein_coding	ENST00000309546	5	3642

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000172	0.470	103181	0	2	103183	0.00000969

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.06	121	158	0.764	0.00000874	1797
Missense in Polyphen		27	36.672	0.73626		386
Synonymous	2.63	47	76.2	0.617	0.00000455	661
Loss of Function	0.299	6	6.84	0.877	2.94e-7	83

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.0000733	0.0000733
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in BCR (B-cell antigen receptor)-mediated signaling in B-cells and TCR (T-cell antigen receptor)-mediated T- cell signaling in T-cells. In absence of TCR signaling, may be involved in CD4-mediated inhibition of T-cell activation. Couples activation of these receptors and their associated kinases with distal intracellular events such as calcium mobilization or MAPK activation through the recruitment of PLCG2, GRB2, GRAP2, and other signaling molecules. {ECO:0000269|PubMed:14610046}.
• Pathway: BCR (Consensus)

Haploinsufficiency Scores

• pHI: 0.101
• hipred: N
• hipred_score: 0.139

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.668

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lime1
• Phenotype: normal phenotype; hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: adaptive immune response;regulation of transcription by RNA polymerase II;regulation of phosphatidylinositol 3-kinase signaling;regulation of I-kappaB kinase/NF-kappaB signaling;regulation of MAP kinase activity;T cell receptor signaling pathway;B cell receptor signaling pathway;regulation of release of sequestered calcium ion into cytosol;regulation of NIK/NF-kappaB signaling
• Cellular component: extracellular space;integral component of membrane;B cell receptor complex
• Molecular function: protein kinase binding