TSC22D1

TSC22 domain family member 1

Basic information

Region (hg38): 13:44432143-44577147

Previous symbols: [ "TGFB1I4" ]

Links

ENSG00000102804 ∙ NCBI:8848 ∙ OMIM:607715 ∙ HGNC:16826 ∙ Uniprot:Q15714 ∙ 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 TSC22D1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSC22D1 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	2	3
missense			13	1		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	2	2

Variants in TSC22D1

This is a list of pathogenic ClinVar variants found in the TSC22D1 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-44434642-G-A		not specified	Uncertain significance (May 13, 2024)
13-44434703-G-T		not specified	Uncertain significance (Nov 29, 2023)
13-44434706-G-A		not specified	Uncertain significance (Nov 15, 2024)
13-44434829-T-C		not specified	Uncertain significance (Jun 28, 2024)
13-44573186-G-C			Likely benign (Jun 01, 2023)
13-44573471-C-A		not specified	Uncertain significance (Sep 27, 2021)
13-44573721-G-A		not specified	Uncertain significance (Jun 11, 2021)
13-44573733-G-C		not specified	Uncertain significance (Jun 11, 2021)
13-44573922-G-A		not specified	Uncertain significance (Aug 17, 2021)
13-44573957-T-C			Benign (Nov 17, 2017)
13-44574217-C-T		not specified	Uncertain significance (Oct 12, 2021)
13-44574563-T-G		not specified	Uncertain significance (Sep 16, 2021)
13-44574598-T-C		not specified	Likely benign (Aug 10, 2021)
13-44574689-C-A		not specified	Uncertain significance (Sep 01, 2021)
13-44575026-C-T		not specified	Uncertain significance (Sep 22, 2021)
13-44575276-T-G		not specified	Uncertain significance (Aug 30, 2021)
13-44575559-G-A			Benign (Nov 17, 2017)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSC22D1	protein_coding	protein_coding	ENST00000458659	3	143629

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.960	0.0401	125741	0	7	125748	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.881	621	562	1.10	0.0000266	6941
Missense in Polyphen		194	210.29	0.92252		2675
Synonymous	-3.28	280	218	1.28	0.0000113	2342
Loss of Function	4.43	5	32.1	0.156	0.00000142	329

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000331	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional repressor. Acts on the C-type natriuretic peptide (CNP) promoter.
• Pathway: Ectoderm Differentiation;POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation;Developmental Biology;POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation;Transcriptional regulation of pluripotent stem cells (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.108
• rvis_EVS: -1.26
• rvis_percentile_EVS: 5.34

Haploinsufficiency Scores

• pHI: 0.542
• hipred: N
• hipred_score: 0.376
• ghis: 0.592

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.672

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tsc22d1
• Phenotype: hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); renal/urinary system phenotype

Gene ontology

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