PDRG1

p53 and DNA damage regulated 1

Basic information

Region (hg38): 20:31944337-31952046

Previous symbols: [ "C20orf126" ]

Links

ENSG00000088356 ∙ NCBI:81572 ∙ OMIM:610789 ∙ HGNC:16119 ∙ Uniprot:Q9NUG6 ∙ 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 PDRG1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDRG1 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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	0	0

Variants in PDRG1

This is a list of pathogenic ClinVar variants found in the PDRG1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-31946567-T-A		not specified	Uncertain significance (Aug 22, 2023)
20-31948816-A-G		not specified	Uncertain significance (Jan 26, 2022)
20-31948841-G-T		not specified	Uncertain significance (Sep 24, 2024)
20-31951904-C-T		not specified	Uncertain significance (Oct 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDRG1	protein_coding	protein_coding	ENST00000202017	5	7138

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000259	0.556	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.427	59	69.0	0.855	0.00000349	867
Missense in Polyphen		19	22.878	0.8305		279
Synonymous	0.503	23	26.3	0.875	0.00000130	240
Loss of Function	0.506	6	7.49	0.801	3.83e-7	89

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000908	0.0000907
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in chaperone-mediated protein folding. {ECO:0000305}.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.643
• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.19

Haploinsufficiency Scores

• pHI: 0.0999
• hipred: N
• hipred_score: 0.282
• ghis: 0.573

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.916

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pdrg1

Gene ontology

• Biological process: protein folding
• Cellular component: cytoplasm;prefoldin complex
• Molecular function: unfolded protein binding