TBRG4

transforming growth factor beta regulator 4, the group of Small nucleolar RNA protein coding host genes|FASTK mitochondrial RNA binding family

Basic information

Region (hg38): 7:45100100-45112047

Links

ENSG00000136270 ∙ NCBI:9238 ∙ OMIM:611325 ∙ HGNC:17443 ∙ Uniprot:Q969Z0 ∙ 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 TBRG4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TBRG4 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			30	2		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	2	2

Variants in TBRG4

This is a list of pathogenic ClinVar variants found in the TBRG4 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-45100357-G-A		not specified	Uncertain significance (Jan 04, 2024)
7-45101278-C-T		not specified	Uncertain significance (Apr 06, 2023)
7-45101365-A-T		not specified	Uncertain significance (Jan 26, 2022)
7-45101537-T-C		not specified	Uncertain significance (Jan 22, 2024)
7-45101573-C-T		not specified	Uncertain significance (Sep 14, 2022)
7-45101585-C-T		not specified	Uncertain significance (Apr 20, 2024)
7-45101588-C-T		not specified	Likely benign (Apr 09, 2024)
7-45101860-C-A		not specified	Uncertain significance (Oct 17, 2023)
7-45101873-C-T		not specified	Uncertain significance (Mar 18, 2024)
7-45101899-T-G		not specified	Uncertain significance (Jan 31, 2024)
7-45101917-A-G		not specified	Uncertain significance (Nov 09, 2022)
7-45101926-A-T		not specified	Uncertain significance (Apr 06, 2023)
7-45101980-G-T		not specified	Uncertain significance (Jan 09, 2024)
7-45101993-C-T		not specified	Uncertain significance (Dec 06, 2022)
7-45101995-G-A		not specified	Uncertain significance (Jan 12, 2024)
7-45102000-C-G		not specified	Uncertain significance (Sep 15, 2021)
7-45102359-T-C		not specified	Uncertain significance (Dec 13, 2021)
7-45102398-C-T		not specified	Uncertain significance (Oct 04, 2022)
7-45103346-T-C		not specified	Uncertain significance (Sep 14, 2022)
7-45103396-G-A			Benign (May 21, 2018)
7-45103412-A-G		not specified	Uncertain significance (Dec 13, 2021)
7-45104634-G-A		not specified	Uncertain significance (Aug 16, 2021)
7-45104658-C-G		not specified	Uncertain significance (Feb 22, 2023)
7-45104663-A-G		not specified	Uncertain significance (Nov 14, 2023)
7-45105454-C-T		not specified	Uncertain significance (May 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TBRG4	protein_coding	protein_coding	ENST00000258770	10	11948

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000122	0.998	125720	0	28	125748	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.866	321	368	0.873	0.0000215	4031
Missense in Polyphen		84	118.22	0.71053		1321
Synonymous	-0.190	168	165	1.02	0.00000991	1352
Loss of Function	2.70	15	31.3	0.479	0.00000187	310

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000193	0.000193
Ashkenazi Jewish	0.00	0.00
East Asian	0.000273	0.000272
Finnish	0.000141	0.000139
European (Non-Finnish)	0.000126	0.000123
Middle Eastern	0.000273	0.000272
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in processing of mitochondrial RNA precursors and in stabilization of a subset of mature mitochondrial RNA species, such as MT-CO1, MT-CO2, MT-CYB, MT-CO3, MT-ND3, MT-ND5 and MT-ATP8/6. May play a role in cell cycle progression (PubMed:9383053). {ECO:0000269|PubMed:28335001, ECO:0000269|PubMed:9383053}.

Recessive Scores

• pRec: 0.0897

Intolerance Scores

• loftool: 0.557
• rvis_EVS: -0.44
• rvis_percentile_EVS: 24.53

Haploinsufficiency Scores

• pHI: 0.0690
• hipred: N
• hipred_score: 0.417
• ghis: 0.536

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.992

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tbrg4

Gene ontology

• Biological process: protein phosphorylation;cell cycle arrest;positive regulation of cell population proliferation;mRNA metabolic process;regulation of mitochondrial mRNA stability;cellular respiration;mitochondrial mRNA processing
• Cellular component: mitochondrion;mitochondrial matrix
• Molecular function: RNA binding;protein kinase activity;protein binding