LCP1

lymphocyte cytosolic protein 1, the group of EF-hand domain containing

Basic information

Region (hg38): 13:46125919-46211871

Links

ENSG00000136167 ∙ NCBI:3936 ∙ OMIM:153430 ∙ HGNC:6528 ∙ Uniprot:P13796 ∙ 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 LCP1 gene.

• Hereditary breast ovarian cancer syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LCP1 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			18		2	20
nonsense	1					1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	1	0	18	0	3

Variants in LCP1

This is a list of pathogenic ClinVar variants found in the LCP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-46127632-C-T		not specified	Uncertain significance (Sep 06, 2022)
13-46127634-G-A		not specified	Uncertain significance (Aug 17, 2022)
13-46127674-G-A		not specified	Uncertain significance (Dec 28, 2022)
13-46127686-C-A		not specified	Uncertain significance (Oct 29, 2021)
13-46130931-T-C		not specified	Uncertain significance (Jul 22, 2022)
13-46130935-G-C			Benign (Dec 31, 2019)
13-46134155-T-C		not specified	Uncertain significance (Sep 07, 2022)
13-46142283-C-A			Benign (Jul 29, 2018)
13-46143339-T-C		not specified	Uncertain significance (Sep 15, 2021)
13-46146960-G-T		Hereditary breast ovarian cancer syndrome	Pathogenic (Aug 01, 2020)
13-46147042-C-T		not specified	Uncertain significance (Jan 08, 2024)
13-46147043-G-A		not specified	Uncertain significance (Nov 18, 2022)
13-46147045-C-G		not specified	Uncertain significance (Apr 06, 2024)
13-46148378-C-T		not specified	Uncertain significance (Apr 04, 2023)
13-46151028-G-T		not specified	Uncertain significance (Mar 12, 2024)
13-46151076-G-T		not specified	Uncertain significance (Jun 16, 2024)
13-46154879-T-C		not specified	Uncertain significance (Jan 31, 2024)
13-46156491-C-T		not specified	Uncertain significance (Jan 30, 2024)
13-46156507-C-T		not specified	Uncertain significance (Jun 22, 2024)
13-46158546-C-T		not specified	Uncertain significance (Dec 19, 2023)
13-46158630-T-C		not specified	Uncertain significance (Nov 03, 2022)
13-46158642-C-T		not specified	Uncertain significance (Jun 07, 2024)
13-46158935-G-A			Benign (Dec 31, 2019)
13-46158959-T-C		not specified	Uncertain significance (Jan 31, 2023)
13-46159641-C-T		not specified	Uncertain significance (Aug 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LCP1	protein_coding	protein_coding	ENST00000398576	15	85952

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.553	0.447	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.72	247	335	0.736	0.0000166	4158
Missense in Polyphen		46	101.85	0.45165		1327
Synonymous	1.16	112	129	0.870	0.00000680	1181
Loss of Function	4.19	7	33.0	0.212	0.00000170	398

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000185	0.000185
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000616	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Actin-binding protein (PubMed:16636079, PubMed:17294403, PubMed:28493397). Plays a role in the activation of T-cells in response to costimulation through TCR/CD3 and CD2 or CD28 (PubMed:17294403). Modulates the cell surface expression of IL2RA/CD25 and CD69 (PubMed:17294403). {ECO:0000269|PubMed:16636079, ECO:0000269|PubMed:17294403, ECO:0000269|PubMed:28493397}.
• Disease: DISEASE: Note=Chromosomal aberrations involving LCP1 is a cause of B-cell non-Hodgkin lymphomas (B-cell NHL). Translocation t(3;13)(q27;q14), with BCL6. {ECO:0000269|PubMed:10469447}.; DISEASE: Note=Defects in LCP1 has been found in a patient with isolated coloboma, a defect of the eye characterized by the absence of ocular structures due to abnormal morphogenesis of the optic cup and stalk, and the fusion of the fetal fissure (optic fissure). Isolated colobomas may be associated with an abnormally small eye (microphthalmia) or small cornea. {ECO:0000269|PubMed:28493397}.
• Pathway: Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation (Consensus)

Recessive Scores

• pRec: 0.288

Intolerance Scores

• loftool: 0.0867
• rvis_EVS: 0.11
• rvis_percentile_EVS: 61.91

Haploinsufficiency Scores

• pHI: 0.641
• hipred: Y
• hipred_score: 0.654
• ghis: 0.534

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.907

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lcp1
• Phenotype: hematopoietic system phenotype; immune system phenotype

Zebrafish Information Network

• Gene name: lcp1
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: viability

Gene ontology

• Biological process: T cell activation involved in immune response;protein kinase A signaling;cell migration;extracellular matrix disassembly;animal organ regeneration;regulation of intracellular protein transport;interleukin-12-mediated signaling pathway;wound healing, spreading of cells;actin filament bundle assembly;actin filament network formation;positive regulation of podosome assembly
• Cellular component: stress fiber;ruffle;phagocytic cup;podosome;extracellular space;cytoplasm;cytosol;actin filament;plasma membrane;focal adhesion;actin cytoskeleton;cell junction;filopodium;actin filament bundle;ruffle membrane;perinuclear region of cytoplasm;extracellular exosome
• Molecular function: actin binding;integrin binding;calcium ion binding;identical protein binding;actin filament binding;GTPase binding