PPARGC1B

PPARG coactivator 1 beta, the group of RNA binding motif containing|MicroRNA protein coding host genes

Basic information

Region (hg38): 5:149730297-149855022

Links

ENSG00000155846 ∙ NCBI:133522 ∙ OMIM:608886 ∙ HGNC:30022 ∙ Uniprot:Q86YN6 ∙ 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 PPARGC1B gene.

• Inborn genetic diseases (49 variants)
• not provided (41 variants)
• PPARGC1B polymorphism (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPARGC1B 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					7	7
missense			46	3	12	61
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					21	21
Total	0	0	46	3	40

Variants in PPARGC1B

This is a list of pathogenic ClinVar variants found in the PPARGC1B region.

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

Position	Type	Phenotype	Significance	ClinVar
5-149730358-T-C		not specified	Uncertain significance (Jun 28, 2023)
5-149730364-G-A		not specified	Uncertain significance (Nov 18, 2022)
5-149730381-G-T		not specified	Uncertain significance (Jan 03, 2024)
5-149730404-A-G		not specified	Uncertain significance (Jan 10, 2022)
5-149771756-C-T			Benign (Jun 19, 2021)
5-149771885-A-T			Benign (Nov 12, 2018)
5-149772144-G-A			Benign (Nov 12, 2018)
5-149820326-G-A			Benign (Jun 20, 2021)
5-149820445-G-A			Benign (Dec 31, 2019)
5-149820479-T-G		not specified	Uncertain significance (Dec 09, 2023)
5-149820480-T-C			Benign (Nov 12, 2018)
5-149820521-C-T		not specified	Uncertain significance (Jan 03, 2022)
5-149820581-G-A		not specified	Uncertain significance (Dec 15, 2022)
5-149820839-A-G			Benign (Jun 19, 2021)
5-149820890-G-C			Benign (Jun 20, 2021)
5-149826377-G-A			Benign (Jun 20, 2021)
5-149826429-G-A			Benign (Jun 20, 2021)
5-149826541-G-A			Benign (Jun 20, 2021)
5-149826700-G-C		not specified	Uncertain significance (Mar 08, 2024)
5-149826736-G-A		not specified	Uncertain significance (Feb 17, 2022)
5-149826745-G-A		not specified	Uncertain significance (Dec 21, 2021)
5-149826794-C-T		not specified	Uncertain significance (Mar 04, 2024)
5-149826811-C-G		not specified	Uncertain significance (Sep 20, 2023)
5-149826828-C-G			Benign (Mar 05, 2018)
5-149826881-C-T		not specified	Uncertain significance (Aug 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPARGC1B	protein_coding	protein_coding	ENST00000309241	12	124725

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.503	0.497	125726	0	22	125748	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.503	566	601	0.942	0.0000362	6582
Missense in Polyphen		143	164.58	0.86888		1848
Synonymous	-0.985	274	254	1.08	0.0000158	2080
Loss of Function	4.89	10	45.7	0.219	0.00000254	499

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000387	0.000304
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000981	0.0000924
European (Non-Finnish)	0.000109	0.000105
Middle Eastern	0.00	0.00
South Asian	0.0000667	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role of stimulator of transcription factors and nuclear receptors activities. Activates transcriptional activity of estrogen receptor alpha, nuclear respiratory factor 1 (NRF1) and glucocorticoid receptor in the presence of glucocorticoids. May play a role in constitutive non-adrenergic-mediated mitochondrial biogenesis as suggested by increased basal oxygen consumption and mitochondrial number when overexpressed. May be involved in fat oxidation and non-oxidative glucose metabolism and in the regulation of energy expenditure. Induces the expression of PERM1 in the skeletal muscle in an ESRRA-dependent manner. {ECO:0000269|PubMed:11854298, ECO:0000269|PubMed:12678921, ECO:0000269|PubMed:15546003, ECO:0000269|PubMed:23836911}.
• Pathway: Insulin resistance - Homo sapiens (human);AMP-activated Protein Kinase (AMPK) Signaling;Energy Metabolism;Sterol Regulatory Element-Binding Proteins (SREBP) signalling;Differentiation of white and brown adipocyte;Mitochondrial Gene Expression;Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways;Prostaglandin Synthesis and Regulation;Transcriptional regulation by RUNX2;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Transcriptional activation of mitochondrial biogenesis;Mitochondrial biogenesis;Regulation of RUNX2 expression and activity;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.214

Intolerance Scores

• loftool: 0.489
• rvis_EVS: 1.06
• rvis_percentile_EVS: 91.47

Haploinsufficiency Scores

• pHI: 0.234
• hipred: Y
• hipred_score: 0.594
• ghis: 0.430

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.846

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppargc1b
• Phenotype: adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; muscle phenotype; cellular phenotype; homeostasis/metabolism phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; respiratory 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); 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); hematopoietic system phenotype; skeleton phenotype

Gene ontology

• Biological process: ossification;regulation of transcription, DNA-templated;mitochondrial transcription;actin filament organization;positive regulation of alkaline phosphatase activity;intracellular estrogen receptor signaling pathway;cellular response to reactive oxygen species;positive regulation of phosphorylation;positive regulation of osteoclast differentiation;positive regulation of bone resorption;negative regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;positive regulation of DNA-binding transcription factor activity;response to glucocorticoid;response to cAMP;bone trabecula formation;positive regulation of cold-induced thermogenesis
• Cellular component: nucleus;nucleoplasm;mitochondrion;mediator complex
• Molecular function: transcription coregulator activity;RNA binding;transcription factor binding;estrogen receptor binding;nuclear receptor transcription coactivator activity;AF-2 domain binding