PACRGL

parkin coregulated like, the group of Armadillo like helical domain containing

Basic information

Region (hg38): 4:20696281-20752907

Previous symbols: [ "C4orf28" ]

Links

ENSG00000163138 ∙ NCBI:133015 ∙ ∙ HGNC:28442 ∙ Uniprot:Q8N7B6 ∙ 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 PACRGL gene.

• Inborn genetic diseases (8 variants)

Variants pathogenicity by type

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

Variants in PACRGL

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

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

Position	Type	Phenotype	Significance	ClinVar
4-20704492-C-T		not specified	Uncertain significance (Jan 23, 2024)
4-20704677-A-C		not specified	Uncertain significance (Dec 03, 2021)
4-20704713-G-A		not specified	Uncertain significance (May 05, 2023)
4-20704716-C-A		not specified	Uncertain significance (Sep 14, 2023)
4-20704723-G-A		not specified	Uncertain significance (Feb 28, 2023)
4-20704740-A-G		not specified	Uncertain significance (Feb 21, 2024)
4-20709767-A-C		not specified	Uncertain significance (Oct 10, 2023)
4-20712842-G-A		not specified	Uncertain significance (Dec 06, 2023)
4-20713436-A-T		not specified	Uncertain significance (Jun 05, 2023)
4-20713526-A-G		not specified	Uncertain significance (Aug 02, 2021)
4-20713534-A-C		not specified	Uncertain significance (Aug 12, 2021)
4-20727315-C-A		not specified	Uncertain significance (Jan 04, 2022)
4-20749655-A-G		KCNIP4-related disorder	Benign (Oct 16, 2019)
4-20749681-T-C		not specified	Uncertain significance (Dec 15, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PACRGL	protein_coding	protein_coding	ENST00000503585	8	56626

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.26e-12	0.0132	125540	0	202	125742	0.000804

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.229	112	119	0.941	0.00000549	1581
Missense in Polyphen		31	30.227	1.0256		426
Synonymous	-0.953	51	43.0	1.18	0.00000209	481
Loss of Function	-0.526	17	14.8	1.15	8.21e-7	190

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000330	0.000330
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.00735	0.00737
Finnish	0.00	0.00
European (Non-Finnish)	0.000415	0.000413
Middle Eastern	0.00735	0.00737
South Asian	0.000294	0.000294
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.391
• rvis_EVS: 0.37
• rvis_percentile_EVS: 75.12

Haploinsufficiency Scores

• pHI: 0.129
• hipred: N
• hipred_score: 0.187
• ghis: 0.514

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pacrgl

Gene ontology

• Molecular function: protein binding