TBRG1

transforming growth factor beta regulator 1

Basic information

Region (hg38): 11:124622836-124635926

Links

ENSG00000154144 ∙ NCBI:84897 ∙ OMIM:610614 ∙ HGNC:29551 ∙ Uniprot:Q3YBR2 ∙ 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 TBRG1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TBRG1 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		1
missense			26			26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	1	0

Variants in TBRG1

This is a list of pathogenic ClinVar variants found in the TBRG1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-124623123-C-T		not specified	Uncertain significance (Sep 19, 2022)
11-124623220-A-C		not specified	Uncertain significance (Aug 22, 2023)
11-124624938-C-T		not specified	Uncertain significance (Feb 06, 2024)
11-124625710-T-G			Likely benign (Mar 01, 2022)
11-124625763-C-T		not specified	Uncertain significance (May 23, 2023)
11-124625810-A-G		not specified	Uncertain significance (Feb 03, 2022)
11-124625897-C-G		not specified	Uncertain significance (Dec 19, 2022)
11-124626518-G-A		not specified	Uncertain significance (Jan 23, 2024)
11-124626542-T-C		not specified	Uncertain significance (Apr 04, 2024)
11-124626940-G-A		Intellectual disability	Likely pathogenic (-)
11-124626940-G-T		not specified	Uncertain significance (Nov 07, 2022)
11-124626952-G-A		not specified	Uncertain significance (Apr 12, 2024)
11-124626953-T-C		not specified	Uncertain significance (Jan 04, 2022)
11-124626971-G-A		not specified	Uncertain significance (Jan 16, 2024)
11-124626976-T-C		not specified	Uncertain significance (Sep 20, 2023)
11-124627045-C-A		not specified	Uncertain significance (Mar 07, 2024)
11-124630425-T-C		not specified	Uncertain significance (Jul 09, 2021)
11-124630448-T-C		not specified	Uncertain significance (May 08, 2024)
11-124630457-G-A		not specified	Uncertain significance (Mar 01, 2023)
11-124630745-G-C		not specified	Uncertain significance (Jan 22, 2024)
11-124630768-T-C		not specified	Uncertain significance (Mar 22, 2023)
11-124631297-G-T		not specified	Uncertain significance (Sep 26, 2023)
11-124631313-A-G		not specified	Uncertain significance (Dec 16, 2022)
11-124631325-C-T		not specified	Uncertain significance (Feb 14, 2024)
11-124631337-C-T		not specified	Likely benign (Mar 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TBRG1	protein_coding	protein_coding	ENST00000441174	9	12556

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000174	0.974	125562	0	31	125593	0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.812	175	208	0.842	0.00000986	2640
Missense in Polyphen		46	55.427	0.82992		745
Synonymous	1.38	65	80.8	0.804	0.00000390	810
Loss of Function	1.99	9	18.2	0.496	9.19e-7	232

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000121	0.000121
Ashkenazi Jewish	0.00	0.00
East Asian	0.000221	0.000218
Finnish	0.0000501	0.0000462
European (Non-Finnish)	0.000169	0.000159
Middle Eastern	0.000221	0.000218
South Asian	0.000146	0.000131
Other	0.000171	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a growth inhibitor. Can activate p53/TP53, causes G1 arrest and collaborates with CDKN2A to restrict proliferation, but does not require either protein to inhibit DNA synthesis. Redistributes CDKN2A into the nucleoplasm. Involved in maintaining chromosomal stability. {ECO:0000269|PubMed:17110379}.

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.593
• rvis_EVS: -0.18
• rvis_percentile_EVS: 39.95

Haploinsufficiency Scores

• pHI: 0.0575
• hipred: N
• hipred_score: 0.410
• ghis: 0.571

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.568

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tbrg1
• 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); immune system phenotype; neoplasm; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype

Gene ontology

• Biological process: DNA replication;cell cycle arrest;negative regulation of cell population proliferation;protein stabilization;protein localization to nucleoplasm
• Cellular component: nucleus
• Molecular function: protein binding