PACRG

parkin coregulated, the group of Armadillo like helical domain containing

Basic information

Region (hg38): 6:162727132-163315500

Links

ENSG00000112530 ∙ NCBI:135138 ∙ OMIM:608427 ∙ HGNC:19152 ∙ Uniprot:Q96M98 ∙ 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 PACRG gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PACRG 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			16	1		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding		2	12	4	2	20
Total	0	2	28	5	4

Variants in PACRG

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

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

Position	Type	Phenotype	Significance	ClinVar
6-162727551-C-T			Likely benign (Aug 17, 2018)
6-162727643-C-G			Likely benign (Jan 27, 2023)
6-162727650-G-T			Uncertain significance (Jan 21, 2022)
6-162727652-A-C			Likely benign (Jul 19, 2022)
6-162727657-C-A			Uncertain significance (May 21, 2018)
6-162727657-C-T			Uncertain significance (Jan 20, 2021)
6-162727658-G-A		Autosomal recessive juvenile Parkinson disease 2	Uncertain significance (Jan 13, 2018)
6-162727661-C-A		Autosomal recessive juvenile Parkinson disease 2	Pathogenic (Mar 01, 2006)
6-162727665-T-C			Uncertain significance (Jan 16, 2018)
6-162727667-A-G		Autosomal recessive juvenile Parkinson disease 2	Pathogenic/Likely pathogenic (Nov 18, 2019)
6-162727668-T-C		Young-onset Parkinson disease	Pathogenic/Likely pathogenic (Jan 02, 2023)
6-162727688-G-A			Uncertain significance (Nov 03, 2021)
6-162727698-A-G		Autosomal recessive juvenile Parkinson disease 2 • PRKN-related disorder	Likely benign (Jun 30, 2020)
6-162727710-A-G		Autosomal recessive juvenile Parkinson disease 2	Uncertain significance (Jan 13, 2018)
6-162727714-G-A		Autosomal recessive juvenile Parkinson disease 2	Uncertain significance (Jan 13, 2018)
6-162727725-C-G		Autosomal recessive juvenile Parkinson disease 2	Uncertain significance (Jan 13, 2018)
6-162727746-G-T		Autosomal recessive juvenile Parkinson disease 2	Uncertain significance (Jan 12, 2018)
6-162727753-C-T		Autosomal recessive juvenile Parkinson disease 2	Uncertain significance (Jan 13, 2018)
6-162727775-C-T		Juvenile-onset Parkinson disease	Uncertain significance (Jun 14, 2016)
6-162727992-T-C			Benign (Jul 05, 2018)
6-162728023-A-C			Benign (Jan 22, 2024)
6-162728252-A-G		not specified	Uncertain significance (Aug 19, 2023)
6-162728267-A-G		not specified	Uncertain significance (Apr 07, 2023)
6-162728276-C-T		not specified	Uncertain significance (Apr 12, 2022)
6-162728307-G-A			Benign (Jun 29, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PACRG	protein_coding	protein_coding	ENST00000337019	6	588361

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.43e-7	0.494	125698	0	50	125748	0.000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.884	130	162	0.804	0.00000881	1928
Missense in Polyphen		51	62.412	0.81715		702
Synonymous	-0.482	70	65.0	1.08	0.00000404	573
Loss of Function	0.850	12	15.6	0.768	0.00000106	162

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000239	0.000239
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000435	0.000435
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000282	0.000281
Middle Eastern	0.000435	0.000435
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Suppresses cell death induced by accumulation of unfolded Pael receptor (Pael-R, a substrate of Parkin). Facilitates the formation of inclusions consisting of Pael-R, molecular chaperones, protein degradation molecules and itself when proteasome is inhibited. May play an important role in the formation of Lewy bodies and protection of dopaminergic neurons against Parkinson disease. {ECO:0000269|PubMed:14532270}.

Recessive Scores

• pRec: 0.173

Intolerance Scores

• loftool: 0.348
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.53

Haploinsufficiency Scores

• pHI: 0.116
• hipred: N
• hipred_score: 0.187
• ghis: 0.556

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.797

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pacrg

Gene ontology

• Biological process: spermatid development;cellular response to unfolded protein;negative regulation of cell death
• Cellular component: nucleus;cytosol;vesicle;neuron projection;cell body;sperm midpiece
• Molecular function: G protein-coupled receptor binding;actin binding;Hsp70 protein binding;heat shock protein binding;ubiquitin protein ligase binding;alpha-tubulin binding;beta-tubulin binding;chaperone binding;Hsp90 protein binding