TSC22D4

TSC22 domain family member 4

Basic information

Region (hg38): 7:100463359-100479232

Links

ENSG00000166925 ∙ NCBI:81628 ∙ OMIM:611914 ∙ HGNC:21696 ∙ Uniprot:Q9Y3Q8 ∙ 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 TSC22D4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSC22D4 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			33	5		38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	5	0

Variants in TSC22D4

This is a list of pathogenic ClinVar variants found in the TSC22D4 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-100463376-A-G		not specified	Uncertain significance (Oct 26, 2021)
7-100463391-T-C		not specified	Uncertain significance (Jun 11, 2021)
7-100463490-TC-T			Uncertain significance (Mar 24, 2022)
7-100463509-C-A		not specified	Uncertain significance (Aug 02, 2021)
7-100466967-A-G		not specified	Uncertain significance (Nov 08, 2024)
7-100466975-T-A		not specified	Uncertain significance (Oct 29, 2021)
7-100466996-C-T		not specified	Uncertain significance (Oct 26, 2023)
7-100467008-G-A		not specified	Uncertain significance (Dec 21, 2023)
7-100467011-G-A		not specified	Uncertain significance (Aug 04, 2024)
7-100467018-G-T		not specified	Uncertain significance (Feb 27, 2023)
7-100467035-G-A		not specified	Uncertain significance (Nov 30, 2021)
7-100467141-C-A		not specified	Uncertain significance (Jul 30, 2024)
7-100467595-G-C		not specified	Uncertain significance (Jul 23, 2024)
7-100474371-T-G		not specified	Uncertain significance (Aug 02, 2021)
7-100477279-G-T		not specified	Uncertain significance (Jan 10, 2023)
7-100477311-C-T		not specified	Uncertain significance (Nov 13, 2024)
7-100477312-G-A		not specified	Uncertain significance (Jan 03, 2024)
7-100477318-G-C		not specified	Uncertain significance (Sep 20, 2024)
7-100477339-G-A		not specified	Uncertain significance (Mar 15, 2024)
7-100477378-C-T		not specified	Uncertain significance (Nov 01, 2022)
7-100477380-G-A		not specified	Likely benign (Jan 31, 2024)
7-100477416-C-T		not specified	Uncertain significance (Jan 19, 2025)
7-100477431-C-T		not specified	Uncertain significance (Oct 08, 2024)
7-100477438-C-A		not specified	Uncertain significance (Jan 21, 2025)
7-100477458-C-T		not specified	Uncertain significance (Oct 05, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSC22D4	protein_coding	protein_coding	ENST00000300181	4	15921

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.961	0.0394	125661	0	2	125663	0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.00	196	240	0.818	0.0000142	2445
Missense in Polyphen		64	87.303	0.73308		864
Synonymous	0.433	104	110	0.947	0.00000674	916
Loss of Function	2.94	0	10.1	0.00	5.14e-7	124

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000909	0.00000880
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional repressor.

Haploinsufficiency Scores

• pHI: 0.310
• hipred: Y
• hipred_score: 0.594
• ghis: 0.614

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.965

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tsc22d4

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;response to osmotic stress;negative regulation of transcription, DNA-templated
• Cellular component: nucleus;cytoplasm
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;protein binding