LCP2

lymphocyte cytosolic protein 2, the group of SH2 domain containing

Basic information

Region (hg38): 5:170246232-170297815

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.

• Inborn genetic diseases (16 variants)
• not specified (11 variants)
• not provided (6 variants)
• Immunodeficiency 81 (3 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.

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			22	1	1	24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					8	8
Total	0	0	22	3	11

Variants in LCP2

This is a list of pathogenic ClinVar variants found in the LCP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-170248719-G-A		not specified	Uncertain significance (Jan 04, 2024)
5-170248735-A-G			Likely benign (Jun 01, 2022)
5-170252350-C-T		not specified	Benign (Jan 24, 2024)
5-170252456-G-A			Uncertain significance (Jul 01, 2022)
5-170252478-T-C		Immunodeficiency 81	Uncertain significance (Nov 17, 2023)
5-170253130-C-T		not specified	Uncertain significance (Feb 23, 2023)
5-170253133-G-A		not specified	Uncertain significance (Apr 07, 2022)
5-170253135-G-C			Benign (Aug 01, 2023)
5-170253142-G-T		not specified	Uncertain significance (Feb 03, 2022)
5-170253185-G-A			Likely benign (Apr 01, 2023)
5-170258124-C-T		not specified	Uncertain significance (Oct 10, 2023)
5-170258154-G-A		not specified	Uncertain significance (Dec 20, 2023)
5-170258159-C-T		not specified	Benign (Jan 24, 2024)
5-170259003-T-C		not specified	Benign (Jan 24, 2024)
5-170261106-C-T		Immunodeficiency 81	Pathogenic (Jun 21, 2021)
5-170261136-G-A		not specified	Uncertain significance (Dec 18, 2023)
5-170261136-G-T			Uncertain significance (Jul 01, 2021)
5-170262515-G-A		not specified	Benign (Jan 24, 2024)
5-170262600-G-C		not specified	Benign (Jan 24, 2024)
5-170262647-G-C		not specified	Uncertain significance (Sep 14, 2022)
5-170262665-G-A		not specified	Uncertain significance (Nov 17, 2022)
5-170262707-G-A		not specified	Uncertain significance (Nov 27, 2023)
5-170262980-G-C		not specified	Uncertain significance (Jun 21, 2023)
5-170266856-G-A		not specified	Uncertain significance (Sep 28, 2023)
5-170267053-T-C		not specified	Uncertain significance (Mar 06, 2023)

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

• 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