HCLS1
Basic information
Region (hg38): 3:121631399-121660927
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (73 variants)
- not_provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the HCLS1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005335.6. 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 | 1 | |||||
missense | 68 | 74 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 68 | 7 | 0 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
HCLS1 | protein_coding | protein_coding | ENST00000314583 | 13 | 29529 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.00000132 | 0.998 | 125699 | 0 | 49 | 125748 | 0.000195 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.0535 | 283 | 280 | 1.01 | 0.0000159 | 3157 |
Missense in Polyphen | 27 | 31.234 | 0.86444 | 288 | ||
Synonymous | 0.467 | 103 | 109 | 0.943 | 0.00000695 | 928 |
Loss of Function | 2.72 | 15 | 31.5 | 0.476 | 0.00000180 | 346 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000357 | 0.000355 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.0000546 | 0.0000544 |
Finnish | 0.0000477 | 0.0000462 |
European (Non-Finnish) | 0.000284 | 0.000281 |
Middle Eastern | 0.0000546 | 0.0000544 |
South Asian | 0.000163 | 0.000163 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Substrate of the antigen receptor-coupled tyrosine kinase. Plays a role in antigen receptor signaling for both clonal expansion and deletion in lymphoid cells. May also be involved in the regulation of gene expression.;
- Pathway
- Tight junction - Homo sapiens (human);Bacterial invasion of epithelial cells - Homo sapiens (human);Shigellosis - Homo sapiens (human);Pathogenic Escherichia coli infection - Homo sapiens (human);Proteoglycans in cancer - Homo sapiens (human);Pathogenic Escherichia coli infection;B Cell Receptor Signaling Pathway;TYROBP Causal Network;BCR;IL5;Fc-epsilon receptor I signaling in mast cells
(Consensus)
Recessive Scores
- pRec
- 0.133
Intolerance Scores
- loftool
- 0.790
- rvis_EVS
- 0.54
- rvis_percentile_EVS
- 81.07
Haploinsufficiency Scores
- pHI
- 0.517
- hipred
- Y
- hipred_score
- 0.706
- ghis
- 0.500
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.901
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | High |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Hcls1
- Phenotype
- hematopoietic system phenotype; immune system phenotype;
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;regulation of transcription, DNA-templated;positive regulation of cell population proliferation;response to hormone;positive regulation of phosphatidylinositol 3-kinase signaling;actin filament polymerization;erythrocyte differentiation;regulation of actin filament polymerization;positive regulation of granulocyte differentiation;positive regulation of peptidyl-serine phosphorylation;intracellular signal transduction;positive regulation of protein import into nucleus;positive regulation of tyrosine phosphorylation of STAT protein;positive regulation of macrophage differentiation;positive regulation of transcription by RNA polymerase II;positive regulation of peptidyl-tyrosine phosphorylation;positive regulation of DNA-binding transcription factor activity;positive regulation of protein kinase B signaling;cellular response to cytokine stimulus;negative regulation of leukocyte apoptotic process;positive regulation of actin cytoskeleton reorganization
- Cellular component
- nucleus;transcription factor complex;cytoplasm;mitochondrion;cytosol;plasma membrane
- Molecular function
- RNA polymerase II transcription factor binding;actin binding;protein binding;SH3 domain binding;protein kinase binding;protein-containing complex binding