PPRC1

PPARG related coactivator 1, the group of RNA binding motif containing

Basic information

Region (hg38): 10:102132993-102150333

Links

ENSG00000148840 ∙ NCBI:23082 ∙ OMIM:617462 ∙ HGNC:30025 ∙ Uniprot:Q5VV67 ∙ 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 PPRC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPRC1 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				14		14
missense			112	13	8	133
nonsense						0
start loss						0
frameshift						0
inframe indel				1	1	2
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	112	28	9

Variants in PPRC1

This is a list of pathogenic ClinVar variants found in the PPRC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-102133075-G-T		not specified	Uncertain significance (Oct 21, 2021)
10-102133082-G-T		not specified	Uncertain significance (Jan 06, 2023)
10-102133087-C-A		PPRC1-related disorder	Likely benign (Jul 01, 2019)
10-102133092-A-G			Likely benign (Oct 01, 2022)
10-102133103-C-T		not specified	Uncertain significance (Jan 04, 2024)
10-102133115-G-A		not specified	Uncertain significance (Jun 07, 2023)
10-102133117-G-C		not specified	Uncertain significance (May 04, 2023)
10-102133129-C-G		not specified	Uncertain significance (Jun 17, 2022)
10-102133145-G-C		not specified	Uncertain significance (May 27, 2022)
10-102133163-G-T		not specified	Uncertain significance (Jun 17, 2022)
10-102133193-C-T		not specified	Uncertain significance (Oct 12, 2021)
10-102133201-G-A		not specified	Uncertain significance (Jan 24, 2023)
10-102137869-C-T		not specified	Uncertain significance (Jan 30, 2024)
10-102137872-G-A		not specified	Likely benign (Oct 12, 2021)
10-102137923-A-G		not specified	Uncertain significance (Jan 17, 2024)
10-102137943-C-T		PPRC1-related disorder	Likely benign (Apr 01, 2023)
10-102137949-C-T		PPRC1-related disorder	Likely benign (Mar 04, 2019)
10-102137953-A-C		not specified	Uncertain significance (Feb 16, 2023)
10-102138012-A-T		not specified	Uncertain significance (Jun 11, 2024)
10-102138671-C-T		not specified	Uncertain significance (Oct 04, 2022)
10-102138693-T-A		not specified	Uncertain significance (May 08, 2023)
10-102138897-C-T		not specified	Uncertain significance (May 18, 2023)
10-102138904-G-A		not specified	Uncertain significance (Dec 08, 2023)
10-102138955-G-A		not specified	Uncertain significance (Jan 10, 2023)
10-102139132-C-T		PPRC1-related disorder	Benign/Likely benign (Feb 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPRC1	protein_coding	protein_coding	ENST00000278070	14	17296

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	2.03e-7	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.244	898	919	0.977	0.0000519	10539
Missense in Polyphen		214	263.67	0.81162		3194
Synonymous	-0.745	382	364	1.05	0.0000193	3755
Loss of Function	6.72	4	60.4	0.0662	0.00000374	675

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.0000549	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.0000549	0.0000544
South Asian	0.0000654	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a coactivator during transcriptional activation of nuclear genes related to mitochondrial biogenesis and cell growth. Involved in the transcription coactivation of CREB and NRF1 target genes. {ECO:0000269|PubMed:11340167, ECO:0000269|PubMed:16908542}.
• Pathway: Energy Metabolism;Mitochondrial Gene Expression;Transcriptional activation of mitochondrial biogenesis;Mitochondrial biogenesis;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.685

Intolerance Scores

• loftool: 0.239
• rvis_EVS: 0.44
• rvis_percentile_EVS: 77.46

Haploinsufficiency Scores

• pHI: 0.431
• hipred: N
• hipred_score: 0.372
• ghis: 0.475

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.960

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pprc1
• Phenotype: embryo 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)

Gene ontology

• Biological process: mitochondrion organization;positive regulation of transcription by RNA polymerase II;positive regulation of DNA-binding transcription factor activity
• Cellular component: nucleus;nucleoplasm
• Molecular function: transcription coregulator activity;RNA binding;transcription factor binding;nuclear receptor transcription coactivator activity