TSLP

thymic stromal lymphopoietin

Basic information

Region (hg38): 5:111070061-111078026

Links

ENSG00000145777 ∙ NCBI:85480 ∙ OMIM:607003 ∙ HGNC:30743 ∙ Uniprot:Q969D9 ∙ 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 TSLP gene.

• Inborn genetic diseases (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSLP gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	0

Variants in TSLP

This is a list of pathogenic ClinVar variants found in the TSLP region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
5-111071925-T-A		not specified	Uncertain significance (Jun 23, 2023)
5-111071960-G-C		not specified	Uncertain significance (Dec 12, 2022)
5-111071993-G-A		not specified	Uncertain significance (Apr 18, 2023)
5-111071998-T-G		not specified	Uncertain significance (Jun 06, 2023)
5-111072897-A-G		not specified	Uncertain significance (Oct 26, 2022)
5-111072919-C-G		not specified	Uncertain significance (Mar 14, 2023)
5-111073569-C-G		not specified	Uncertain significance (Oct 05, 2021)
5-111076004-G-C		not specified	Uncertain significance (Nov 21, 2023)
5-111076012-C-A		not specified	Uncertain significance (Jan 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSLP	protein_coding	protein_coding	ENST00000344895	4	7963

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00404	0.668	125735	0	12	125747	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.491	100	87.1	1.15	0.00000423	1038
Missense in Polyphen		28	22.662	1.2355		282
Synonymous	-1.68	45	32.8	1.37	0.00000159	294
Loss of Function	0.602	4	5.53	0.724	2.32e-7	69

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000547	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000882	0.0000879
Middle Eastern	0.0000547	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Isoform 1: Cytokine that induces the release of T-cell- attracting chemokines from monocytes and, in particular, enhances the maturation of CD11c(+) dendritic cells. Can induce allergic inflammation by directly activating mast cells. {ECO:0000269|PubMed:11418668, ECO:0000269|PubMed:11480573, ECO:0000269|PubMed:17242164}.
• Pathway: Jak-STAT signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);JAK-STAT-Core;Thymic Stromal LymphoPoietin (TSLP) Signaling Pathway;Development and heterogeneity of the ILC family (Consensus)

Recessive Scores

• pRec: 0.0705

Intolerance Scores

• loftool: 0.373
• rvis_EVS: -0.27
• rvis_percentile_EVS: 33.97

Haploinsufficiency Scores

• pHI: 0.141
• hipred: N
• hipred_score: 0.221
• ghis: 0.450

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.914

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Low	Low
Primary Immunodeficiency	Medium	Low	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Tslp
• Phenotype: immune system phenotype; digestive/alimentary phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; respiratory system phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: positive regulation of cytokine-mediated signaling pathway;positive regulation of cell population proliferation;regulation of signaling receptor activity;positive regulation of chemokine production;positive regulation of interleukin-10 production;positive regulation of interleukin-13 production;positive regulation of interleukin-5 production;positive regulation of interleukin-6 production;positive regulation of mast cell activation;interleukin-7-mediated signaling pathway;positive regulation of tyrosine phosphorylation of STAT protein;negative regulation of apoptotic process;positive regulation of inflammatory response;positive regulation of chemokine (C-C motif) ligand 1 production;positive regulation of granulocyte colony-stimulating factor production;positive regulation of STAT cascade;positive regulation of interleukin-5 secretion
• Cellular component: extracellular region;extracellular space
• Molecular function: cytokine activity;interleukin-7 receptor binding