THEMIS2

thymocyte selection associated family member 2

Basic information

Region (hg38): 1:27872542-27886685

Previous symbols: [ "C1orf38" ]

Links

ENSG00000130775 ∙ NCBI:9473 ∙ OMIM:617856 ∙ HGNC:16839 ∙ Uniprot:Q5TEJ8 ∙ 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 THEMIS2 gene.

• Inborn genetic diseases (25 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the THEMIS2 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			24	2	1	27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	2	1

Variants in THEMIS2

This is a list of pathogenic ClinVar variants found in the THEMIS2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-27872579-C-T		not specified	Uncertain significance (Dec 22, 2023)
1-27876597-A-G		not specified	Uncertain significance (Aug 02, 2021)
1-27876660-G-A		not specified	Uncertain significance (Dec 01, 2022)
1-27879709-A-C		not specified	Uncertain significance (Dec 13, 2023)
1-27879739-T-C			Benign (Feb 22, 2018)
1-27879782-C-T		not specified	Uncertain significance (Jan 31, 2024)
1-27879784-G-A		not specified	Uncertain significance (Apr 13, 2022)
1-27879794-T-C		not specified	Likely benign (Nov 18, 2022)
1-27879796-C-G		not specified	Uncertain significance (Jun 11, 2021)
1-27879833-G-A		not specified	Uncertain significance (Aug 28, 2023)
1-27879886-C-G		not specified	Uncertain significance (Dec 14, 2023)
1-27879901-G-C		not specified	Uncertain significance (May 15, 2023)
1-27879979-G-A		not specified	Uncertain significance (Dec 21, 2022)
1-27880022-G-A		not specified	Uncertain significance (Jul 20, 2022)
1-27881974-G-T		not specified	Uncertain significance (Nov 03, 2022)
1-27882012-G-A		not specified	Uncertain significance (Jul 13, 2022)
1-27882199-A-G		not specified	Uncertain significance (Feb 05, 2024)
1-27882246-C-G		not specified	Uncertain significance (Sep 30, 2021)
1-27882304-G-A			Uncertain significance (Oct 20, 2022)
1-27882318-C-T		not specified	Uncertain significance (Sep 28, 2022)
1-27882322-C-T		not specified	Uncertain significance (Sep 06, 2022)
1-27882396-G-A		not specified	Uncertain significance (Dec 09, 2023)
1-27882400-G-A		not specified	Uncertain significance (Sep 07, 2022)
1-27882421-C-T		not specified	Uncertain significance (May 11, 2022)
1-27882526-A-G		not specified	Uncertain significance (Mar 16, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
THEMIS2	protein_coding	protein_coding	ENST00000373921	6	14142

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00202	0.994	125711	0	37	125748	0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.24	309	377	0.821	0.0000224	4134
Missense in Polyphen		104	143.18	0.72638		1646
Synonymous	1.07	140	157	0.891	0.00000871	1362
Loss of Function	2.52	8	20.3	0.395	9.29e-7	249

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000219	0.000210
Ashkenazi Jewish	0.000124	0.0000992
East Asian	0.0000561	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000213	0.000211
Middle Eastern	0.0000561	0.0000544
South Asian	0.000131	0.000131
Other	0.000331	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May constitute a control point in macrophage inflammatory response, promoting LPS-induced TNF production. {ECO:0000269|PubMed:20644716}.

Recessive Scores

• pRec: 0.0906

Intolerance Scores

• rvis_EVS: -0.53
• rvis_percentile_EVS: 20.78

Haploinsufficiency Scores

• pHI: 0.543
• hipred: N
• hipred_score: 0.270
• ghis: 0.529

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Themis2
• Phenotype: homeostasis/metabolism phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: inflammatory response;cell adhesion;T cell receptor signaling pathway
• Cellular component: nucleus;cytoplasm
• Molecular function: protein binding