TGFB1I1

transforming growth factor beta 1 induced transcript 1, the group of LIM domain containing

Basic information

Region (hg38): 16:31471585-31477960

Links

ENSG00000140682 ∙ NCBI:7041 ∙ OMIM:602353 ∙ HGNC:11767 ∙ Uniprot:O43294 ∙ 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 TGFB1I1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TGFB1I1 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			33
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	0	0

Variants in TGFB1I1

This is a list of pathogenic ClinVar variants found in the TGFB1I1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-31473506-C-A		not specified	Uncertain significance (Aug 12, 2022)
16-31473507-G-A		not specified	Uncertain significance (Sep 15, 2021)
16-31473518-C-A		not specified	Uncertain significance (Jul 05, 2023)
16-31473835-C-G		not specified	Uncertain significance (Jun 27, 2022)
16-31473837-C-T		not specified	Uncertain significance (May 04, 2022)
16-31473902-G-A		not specified	Uncertain significance (Mar 21, 2024)
16-31473917-G-A		not specified	Uncertain significance (Jun 21, 2023)
16-31473920-C-G		not specified	Uncertain significance (Sep 17, 2021)
16-31474184-G-A		not specified	Uncertain significance (Dec 09, 2023)
16-31474200-A-G		not specified	Uncertain significance (Jan 04, 2024)
16-31474232-C-G		not specified	Uncertain significance (May 03, 2023)
16-31474236-G-A		not specified	Uncertain significance (Jan 24, 2023)
16-31474237-C-A		not specified	Uncertain significance (Jan 24, 2023)
16-31474355-C-G		not specified	Uncertain significance (Aug 18, 2021)
16-31474375-C-G		not specified	Uncertain significance (Jan 26, 2022)
16-31474569-G-C		not specified	Uncertain significance (Apr 13, 2022)
16-31476105-G-A		not specified	Uncertain significance (May 26, 2024)
16-31476109-G-A		not specified	Uncertain significance (Dec 17, 2023)
16-31476146-C-G		not specified	Uncertain significance (Sep 20, 2023)
16-31476148-C-G		not specified	Uncertain significance (Feb 16, 2023)
16-31476168-A-G		not specified	Uncertain significance (Mar 20, 2024)
16-31476513-C-G		not specified	Uncertain significance (Feb 14, 2024)
16-31476532-G-T		not specified	Uncertain significance (Jan 03, 2024)
16-31476892-G-A		not specified	Uncertain significance (Sep 27, 2022)
16-31476905-C-G		not specified	Uncertain significance (Nov 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TGFB1I1	protein_coding	protein_coding	ENST00000394863	11	6376

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0270	0.973	125710	0	19	125729	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.55	225	301	0.748	0.0000187	2954
Missense in Polyphen		102	140.97	0.72355		1384
Synonymous	1.21	113	131	0.865	0.00000888	948
Loss of Function	3.07	7	22.8	0.307	0.00000117	248

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000121	0.000120
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000113	0.0000967
Middle Eastern	0.000109	0.000109
South Asian	0.0000990	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as a molecular adapter coordinating multiple protein-protein interactions at the focal adhesion complex and in the nucleus. Links various intracellular signaling modules to plasma membrane receptors and regulates the Wnt and TGFB signaling pathways. May also regulate SLC6A3 and SLC6A4 targeting to the plasma membrane hence regulating their activity. In the nucleus, functions as a nuclear receptor coactivator regulating glucocorticoid, androgen, mineralocorticoid and progesterone receptor transcriptional activity. May play a role in the processes of cell growth, proliferation, migration, differentiation and senescence. May have a zinc-dependent DNA- binding activity. {ECO:0000269|PubMed:10075738, ECO:0000269|PubMed:11463817, ECO:0000269|PubMed:11856738, ECO:0000269|PubMed:12177201, ECO:0000269|PubMed:12445807, ECO:0000269|PubMed:12700349, ECO:0000269|PubMed:15211577, ECO:0000269|PubMed:15561701, ECO:0000269|PubMed:16141357, ECO:0000269|PubMed:16624805, ECO:0000269|PubMed:16803896, ECO:0000269|PubMed:16849583, ECO:0000269|PubMed:17166536, ECO:0000269|PubMed:17233630, ECO:0000269|PubMed:9032249}.
• Pathway: Androgen receptor signaling pathway;Serotonin Transporter Activity;TGF-beta Signaling Pathway;Monoamine Transport;AndrogenReceptor;Coregulation of Androgen receptor activity (Consensus)

Recessive Scores

• pRec: 0.141

Intolerance Scores

• loftool: 0.340
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.25

Haploinsufficiency Scores

• pHI: 0.820
• hipred: Y
• hipred_score: 0.731
• ghis: 0.655

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.973

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tgfb1i1
• Phenotype: neoplasm; 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); homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); muscle phenotype

Gene ontology

• Biological process: transcription by RNA polymerase II;cell adhesion;negative regulation of cell population proliferation;response to heat;positive regulation of epithelial to mesenchymal transition;Wnt signaling pathway;morphogenesis of embryonic epithelium;positive regulation of transforming growth factor beta receptor signaling pathway;negative regulation of transforming growth factor beta receptor signaling pathway;androgen receptor signaling pathway;ubiquitin-dependent SMAD protein catabolic process;epithelial cell differentiation;cell fate commitment;negative regulation of fat cell differentiation;positive regulation of transcription, DNA-templated
• Cellular component: cytoplasm;cytoskeleton;focal adhesion;nuclear matrix;collagen-containing extracellular matrix
• Molecular function: transcription coactivator activity;protein binding;metal ion binding;Roundabout binding;androgen receptor binding;I-SMAD binding