LCP1
lymphocyte cytosolic protein 1, the group of EF-hand domain containing
Basic information
Region (hg38): 13:46125920-46211871
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- 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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 49 | 52 | ||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 1 | 0 | 49 | 1 | 2 |
Loading clinvar variants...
GnomAD
Source:
| 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:
- 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
| 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