LCP1

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

Basic information

Region (hg38): 13:46125920-46211871

Links

ENSG00000136167NCBI:3936OMIM:153430HGNC:6528Uniprot:P13796AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LCP1 gene.

  • not_specified (50 variants)
  • not_provided (3 variants)
  • 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. These statistics are base on transcript: NM_000002298.5. 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.

EffectPLPVUSLBBSum
synonymous
0
missense
49
clinvar
1
clinvar
2
clinvar
52
nonsense
1
clinvar
1
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 1 0 49 1 2
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
LCP1protein_codingprotein_codingENST00000398576 1585952
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.5530.4471257350131257480.0000517
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.722473350.7360.00001664158
Missense in Polyphen46101.850.451651327
Synonymous1.161121290.8700.000006801181
Loss of Function4.19733.00.2120.00000170398

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001850.000185
Ashkenazi Jewish0.00009920.0000992
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00006160.0000615
Middle Eastern0.000.00
South Asian0.00003270.0000327
Other0.0001630.000163

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
essential_gene_gene_trap
gene_indispensability_pred
E
gene_indispensability_score
0.907

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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