THEMIS

thymocyte selection associated

Basic information

Region (hg38): 6:127708072-127918631

Previous symbols: [ "C6orf207", "C6orf190", "TSEPA" ]

Links

ENSG00000172673 ∙ NCBI:387357 ∙ OMIM:613607 ∙ HGNC:21569 ∙ Uniprot:Q8N1K5 ∙ 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 THEMIS gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the THEMIS 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			40	3	1	44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	40	4	1

Variants in THEMIS

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

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

Position	Type	Phenotype	Significance	ClinVar
6-127719690-G-T		not specified	Uncertain significance (Jul 12, 2022)
6-127719733-C-T		not specified	Uncertain significance (Jan 02, 2024)
6-127719787-T-G		not specified	Uncertain significance (Aug 08, 2022)
6-127719805-T-A		not specified	Likely benign (Jul 26, 2021)
6-127719813-A-C		not specified	Uncertain significance (Nov 30, 2022)
6-127719814-C-T		not specified	Uncertain significance (Mar 01, 2024)
6-127719822-C-T		not specified	Uncertain significance (Dec 06, 2022)
6-127812890-G-A			Likely benign (Jan 22, 2018)
6-127812901-G-T		not specified	Uncertain significance (Jun 16, 2024)
6-127812908-G-A		not specified	Uncertain significance (Jan 23, 2024)
6-127812968-G-A		not specified	Uncertain significance (Jun 21, 2023)
6-127812983-G-A		not specified	Uncertain significance (Dec 02, 2021)
6-127813073-G-A		not specified	Uncertain significance (Mar 03, 2022)
6-127813118-C-A		not specified	Uncertain significance (May 27, 2022)
6-127813143-C-T		not specified	Uncertain significance (Apr 18, 2024)
6-127813169-A-T		not specified	Uncertain significance (Jun 09, 2022)
6-127813247-T-G		not specified	Uncertain significance (Dec 14, 2022)
6-127813266-C-T		not specified	Uncertain significance (Oct 06, 2022)
6-127813268-T-C		not specified	Uncertain significance (Sep 22, 2023)
6-127813370-G-A		not specified	Uncertain significance (May 10, 2024)
6-127813385-T-A		not specified	Uncertain significance (Aug 21, 2023)
6-127813389-T-C		not specified	Uncertain significance (Jun 18, 2021)
6-127813413-C-T		not specified	Uncertain significance (Jun 26, 2023)
6-127813506-T-C		not specified	Likely benign (Feb 28, 2023)
6-127813527-C-T		not specified	Uncertain significance (Jul 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
THEMIS	protein_coding	protein_coding	ENST00000543064	7	210560

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000196	0.973	125701	0	47	125748	0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.583	381	350	1.09	0.0000182	4457
Missense in Polyphen		118	114.92	1.0268		1498
Synonymous	-1.49	151	129	1.17	0.00000712	1308
Loss of Function	2.05	13	23.8	0.546	0.00000115	341

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000297	0.000297
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000397	0.000281
Middle Eastern	0.000164	0.000163
South Asian	0.0000653	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a central role in late thymocyte development by controlling both positive and negative T-cell selection. Required to sustain and/or integrate signals required for proper lineage commitment and maturation of T-cells. Regulates T-cell development through T-cell antigen receptor (TCR) signaling and in particular through the regulation of calcium influx and phosphorylation of Erk. {ECO:0000250|UniProtKB:Q8BGW0}.

Intolerance Scores

• loftool: 0.847
• rvis_EVS: -0.35
• rvis_percentile_EVS: 29.49

Haploinsufficiency Scores

• pHI: 0.160
• hipred: Y
• hipred_score: 0.550
• ghis: 0.437

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0298

Gene Damage Prediction

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

Mouse Genome Informatics

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

Gene ontology

• Biological process: adaptive immune response;positive T cell selection;negative T cell selection;T cell receptor signaling pathway
• Cellular component: nucleus;cytoplasm;cell-cell junction;COP9 signalosome
• Molecular function: protein binding