HCLS1

hematopoietic cell-specific Lyn substrate 1

Basic information

Region (hg38): 3:121631399-121660927

Links

ENSG00000180353

∙ NCBI:3059 ∙ OMIM:601306 ∙ HGNC:4844 ∙ Uniprot:P14317 ∙ 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 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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
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

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: 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

	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