HCLS1

hematopoietic cell-specific Lyn substrate 1

Basic information

Region (hg38): 3:121631399-121660927

Links

ENSG00000180353NCBI:3059OMIM:601306HGNC:4844Uniprot:P14317AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HCLS1 gene.

  • 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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
1
missense
68
clinvar
6
clinvar
74
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 68 7 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
HCLS1protein_codingprotein_codingENST00000314583 1329529
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.000001320.9981256990491257480.000195
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.05352832801.010.00001593157
Missense in Polyphen2731.2340.86444288
Synonymous0.4671031090.9430.00000695928
Loss of Function2.721531.50.4760.00000180346

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003570.000355
Ashkenazi Jewish0.000.00
East Asian0.00005460.0000544
Finnish0.00004770.0000462
European (Non-Finnish)0.0002840.000281
Middle Eastern0.00005460.0000544
South Asian0.0001630.000163
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumHigh
CancerMediumMediumMedium

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