SIT1

signaling threshold regulating transmembrane adaptor 1

Basic information

Region (hg38): 9:35649295-35650931

Links

ENSG00000137078 ∙ NCBI:27240 ∙ OMIM:604964 ∙ HGNC:17710 ∙ Uniprot:Q9Y3P8 ∙ 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 SIT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SIT1 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				1		1
missense			14	1		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	2	0

Variants in SIT1

This is a list of pathogenic ClinVar variants found in the SIT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-35649898-C-T		not specified	Uncertain significance (Sep 30, 2024)
9-35649946-C-T		not specified	Uncertain significance (Jun 18, 2024)
9-35649972-T-C		not specified	Uncertain significance (Dec 24, 2024)
9-35650004-G-A			Likely benign (Aug 14, 2018)
9-35650027-G-A		not specified	Uncertain significance (Jun 29, 2023)
9-35650065-A-G		not specified	Uncertain significance (Nov 02, 2023)
9-35650197-C-T		not specified	Uncertain significance (Jan 17, 2024)
9-35650200-A-G		not specified	Likely benign (Apr 20, 2024)
9-35650227-G-A		not specified	Uncertain significance (Nov 27, 2023)
9-35650243-G-A		not specified	Uncertain significance (Oct 17, 2023)
9-35650389-G-A		not specified	Uncertain significance (Dec 28, 2023)
9-35650503-G-A		not specified	Uncertain significance (Jan 06, 2023)
9-35650514-G-C		not specified	Uncertain significance (Nov 10, 2024)
9-35650553-T-A		not specified	Uncertain significance (Aug 14, 2024)
9-35650613-C-A		not specified	Uncertain significance (Jul 16, 2024)
9-35650802-A-G		not specified	Uncertain significance (May 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SIT1	protein_coding	protein_coding	ENST00000259608	5	1646

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000965	0.824	125647	0	94	125741	0.000374

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.17	79	114	0.692	0.00000678	1202
Missense in Polyphen		15	31.491	0.47633		357
Synonymous	0.153	48	49.4	0.972	0.00000294	416
Loss of Function	1.16	6	9.96	0.603	4.24e-7	111

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00402	0.00403
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Negatively regulates TCR (T-cell antigen receptor)- mediated signaling in T-cells. Involved in positive selection of T-cells. {ECO:0000269|PubMed:10209036}.
• Pathway: TCR (Consensus)

Recessive Scores

• pRec: 0.0998

Intolerance Scores

• loftool: 0.230
• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.23

Haploinsufficiency Scores

• pHI: 0.150
• hipred: N
• hipred_score: 0.461
• ghis: 0.482

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.925

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sit1
• Phenotype: hematopoietic system phenotype; immune system phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: adaptive immune response;signal transduction;T cell homeostasis;regulation of T cell activation
• Cellular component: plasma membrane;integral component of plasma membrane;extracellular exosome
• Molecular function: protein binding;kinase binding;SH2 domain binding