TSC22D2

TSC22 domain family member 2

Basic information

Region (hg38): 3:150408298-150466422

Links

ENSG00000196428 ∙ NCBI:9819 ∙ OMIM:617724 ∙ HGNC:29095 ∙ Uniprot:O75157 ∙ 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 TSC22D2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSC22D2 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				2		2
missense			44	1		45
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	44	3	0

Variants in TSC22D2

This is a list of pathogenic ClinVar variants found in the TSC22D2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-150409358-A-G		not specified	Uncertain significance (Jul 20, 2021)
3-150409423-A-G		not specified	Uncertain significance (Aug 29, 2023)
3-150409510-G-A		not specified	Uncertain significance (Apr 08, 2022)
3-150409580-A-T		not specified	Uncertain significance (Dec 03, 2021)
3-150409589-C-A		not specified	Uncertain significance (Mar 20, 2024)
3-150409631-T-A		not specified	Uncertain significance (Dec 17, 2021)
3-150409667-G-T		not specified	Uncertain significance (Sep 06, 2022)
3-150409687-G-C		not specified	Uncertain significance (Apr 27, 2022)
3-150409687-G-T		not specified	Uncertain significance (Jun 29, 2023)
3-150409703-C-A		not specified	Uncertain significance (Jul 26, 2022)
3-150409716-G-A			Likely benign (Apr 01, 2022)
3-150409741-C-G		not specified	Uncertain significance (Nov 10, 2022)
3-150409742-C-G		not specified	Uncertain significance (Feb 21, 2024)
3-150409764-G-C		not specified	Uncertain significance (Apr 27, 2022)
3-150409858-G-T		not specified	Uncertain significance (Mar 06, 2023)
3-150409965-C-A		not specified	Uncertain significance (Apr 12, 2024)
3-150409970-C-T		not specified	Uncertain significance (Mar 17, 2023)
3-150410002-C-T			Likely benign (Mar 01, 2023)
3-150410081-G-C		not specified	Uncertain significance (Feb 27, 2023)
3-150410098-T-C		not specified	Uncertain significance (May 09, 2023)
3-150410110-C-G		not specified	Uncertain significance (May 13, 2024)
3-150410111-C-T		not specified	Uncertain significance (Apr 19, 2023)
3-150410138-C-T		not specified	Uncertain significance (Sep 16, 2021)
3-150410222-C-T		not specified	Uncertain significance (Oct 26, 2022)
3-150410267-T-C		not specified	Uncertain significance (Jan 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSC22D2	protein_coding	protein_coding	ENST00000361875	4	58097

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.969	0.0315	125716	0	9	125725	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.701	395	436	0.906	0.0000202	4925
Missense in Polyphen		39	56.195	0.69401		555
Synonymous	-1.37	216	192	1.13	0.00000947	1746
Loss of Function	3.97	3	23.9	0.125	0.00000113	252

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000793	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0782

Intolerance Scores

• loftool: 0.108
• rvis_EVS: 0.22
• rvis_percentile_EVS: 68.38

Haploinsufficiency Scores

• pHI: 0.482
• hipred: Y
• hipred_score: 0.572
• ghis: 0.426

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0998

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tsc22d2

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;response to osmotic stress
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific