PRADC1

protease associated domain containing 1

Basic information

Region (hg38): 2:73228009-73233239

Previous symbols: [ "C2orf7" ]

Links

ENSG00000135617 ∙ NCBI:84279 ∙ OMIM:619674 ∙ HGNC:16047 ∙ Uniprot:Q9BSG0 ∙ 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 PRADC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRADC1 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				1		1
missense			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	1	0

Variants in PRADC1

This is a list of pathogenic ClinVar variants found in the PRADC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-73228468-A-G		not specified	Uncertain significance (Mar 07, 2024)
2-73228473-G-A		not specified	Uncertain significance (Jun 04, 2024)
2-73228515-G-T		not specified	Uncertain significance (Jan 26, 2022)
2-73228537-G-A		not specified	Uncertain significance (May 06, 2024)
2-73228568-C-T		not specified	Uncertain significance (Jan 08, 2024)
2-73228824-G-T			Likely benign (Nov 01, 2022)
2-73228829-C-T		not specified	Uncertain significance (May 29, 2024)
2-73228912-C-T		not specified	Uncertain significance (Jul 09, 2021)
2-73228913-G-A		not specified	Uncertain significance (Nov 23, 2021)
2-73229465-T-C		not specified	Uncertain significance (Nov 15, 2023)
2-73229501-C-T		not specified	Uncertain significance (Jun 11, 2024)
2-73229537-C-A		not specified	Uncertain significance (Jul 27, 2021)
2-73229537-C-T		not specified	Uncertain significance (Dec 28, 2022)
2-73230139-G-T		not specified	Uncertain significance (Jun 17, 2024)
2-73230168-C-T		not specified	Uncertain significance (May 25, 2022)
2-73233151-C-T		not specified	Uncertain significance (Feb 10, 2022)
2-73233156-A-G		not specified	Uncertain significance (May 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRADC1	protein_coding	protein_coding	ENST00000258083	5	5233

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000141	0.415	125673	0	75	125748	0.000298

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.531	100	116	0.861	0.00000694	1223
Missense in Polyphen		33	40.9	0.80685		404
Synonymous	0.186	45	46.6	0.965	0.00000295	377
Loss of Function	0.395	8	9.30	0.860	5.47e-7	89

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000305	0.000304
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00250	0.00250
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000655	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.124

Intolerance Scores

• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.64

Haploinsufficiency Scores

• pHI: 0.434
• hipred: N
• hipred_score: 0.350
• ghis: 0.513

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pradc1
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Cellular component: extracellular region
• Molecular function: protein binding