LCP2

lymphocyte cytosolic protein 2, the group of SH2 domain containing

Basic information

Region (hg38): 5:170246233-170297815

Previous symbols: [ "SLP76" ]

Links

ENSG00000043462

∙ NCBI:3937 ∙ OMIM:601603 ∙ HGNC:6529 ∙ Uniprot:Q13094 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

immunodeficiency 81 (Limited), mode of inheritance: AR
immunodeficiency 81 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Immunodeficiency 81	AR	Allergy/Immunology/Infectious; Hematologic	The condition may involve severe, early-onset infections, and preventative measures and early and aggressive treatment of infections may be beneficial; The condition may involve autoimmune hemolytic anemia, and response to steroid treatment has been described; HSCT has been described	Allergy/Immunology/Infectious	33231617

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LCP2 gene.

not_specified (57 variants)
not_provided (9 variants)
Immunodeficiency_81 (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LCP2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005565.5. 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				3 clinvar		3
missense			62 clinvar	1 clinvar	1 clinvar	64
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)	1 clinvar					1
Total	1	0	62	4	1

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LCP2	protein_coding	protein_coding	ENST00000046794	21	51991

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.925	0.0753	124628	0	10	124638	0.0000401

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.918	243	287	0.847	0.0000158	3467
Missense in Polyphen		49	98.256	0.4987		1153
Synonymous	1.10	96	111	0.867	0.00000676	978
Loss of Function	4.52	6	34.7	0.173	0.00000180	433

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000935	0.0000936
Ashkenazi Jewish	0.0000994	0.0000994
East Asian	0.00	0.00
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.0000454	0.0000442
Middle Eastern	0.00	0.00
South Asian	0.0000329	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Involved in T-cell antigen receptor mediated signaling.;
Pathway: Platelet activation - Homo sapiens (human);T cell receptor signaling pathway - Homo sapiens (human);Fc epsilon RI signaling pathway - Homo sapiens (human);Rap1 signaling pathway - Homo sapiens (human);Natural killer cell mediated cytotoxicity - Homo sapiens (human);Osteoclast differentiation - Homo sapiens (human);Fc Epsilon Receptor I Signaling in Mast Cells;T-Cell antigen Receptor (TCR) pathway during Staphylococcus aureus infection;T-Cell antigen Receptor (TCR) Signaling Pathway;DAP12 signaling;DAP12 interactions;Generation of second messenger molecules;TCR signaling;FCERI mediated MAPK activation;FCERI mediated Ca+2 mobilization;Fc epsilon receptor (FCERI) signaling;TCR;Innate Immune System;Immune System;Adaptive Immune System;BCR;GPVI-mediated activation cascade;Platelet activation, signaling and aggregation;Hemostasis;Fc-epsilon receptor I signaling in mast cells;TCR signaling in naïve CD8+ T cells;JNK signaling in the CD4+ TCR pathway;TCR signaling in naïve CD4+ T cells (Consensus)

Recessive Scores

pRec: 0.287

Intolerance Scores

loftool
rvis_EVS: -0.49
rvis_percentile_EVS: 22.65

Haploinsufficiency Scores

pHI: 0.267
hipred: Y
hipred_score: 0.701
ghis: 0.581

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.118

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Lcp2
Phenotype: digestive/alimentary phenotype; immune system phenotype; liver/biliary system phenotype; respiratory system phenotype; hematopoietic 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); homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype;

Gene ontology

Biological process: immune response;transmembrane receptor protein tyrosine kinase signaling pathway;platelet activation;intracellular signal transduction;Fc-epsilon receptor signaling pathway;mast cell activation;positive regulation of protein kinase activity;cytokine secretion;T cell receptor signaling pathway
Cellular component: cytosol;cell-cell junction;TCR signalosome;plasma membrane raft
Molecular function: protein binding