PKDREJ

polycystin family receptor for egg jelly

Basic information

Region (hg38): 22:46255662-46263343

Links

ENSG00000130943 ∙ NCBI:10343 ∙ OMIM:604670 ∙ HGNC:9015 ∙ Uniprot:Q9NTG1 ∙ 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 PKDREJ gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PKDREJ 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				4		4
missense			117	10		127
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	117	14	0

Variants in PKDREJ

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

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

Position	Type	Phenotype	Significance	ClinVar
22-46256640-G-C		not specified	Uncertain significance (Feb 02, 2024)
22-46256646-C-G		not specified	Uncertain significance (Jan 23, 2023)
22-46256661-A-G		not specified	Likely benign (May 03, 2024)
22-46256674-G-C		not specified	Uncertain significance (Nov 27, 2023)
22-46256715-A-G		not specified	Uncertain significance (Nov 06, 2023)
22-46256895-T-C		not specified	Likely benign (Jun 18, 2021)
22-46256928-C-T		not specified	Uncertain significance (Dec 19, 2023)
22-46256995-C-A		not specified	Uncertain significance (Sep 27, 2022)
22-46257011-C-G		not specified	Uncertain significance (Aug 12, 2021)
22-46257019-C-T		not specified	Uncertain significance (Jan 03, 2022)
22-46257040-C-T		not specified	Uncertain significance (Feb 02, 2022)
22-46257065-G-A			Likely benign (Jul 01, 2022)
22-46257117-G-A		not specified	Uncertain significance (May 30, 2024)
22-46257124-T-C		not specified	Uncertain significance (Jun 24, 2022)
22-46257210-A-G		not specified	Uncertain significance (Sep 28, 2022)
22-46257228-G-A		not specified	Uncertain significance (Nov 12, 2021)
22-46257309-A-G		not specified	Uncertain significance (Jul 27, 2022)
22-46257369-A-T		not specified	Uncertain significance (May 27, 2022)
22-46257379-C-T		not specified	Uncertain significance (Jul 26, 2022)
22-46257422-C-G		not specified	Uncertain significance (Dec 20, 2023)
22-46257426-T-C		not specified	Uncertain significance (Jan 09, 2024)
22-46257442-C-A		not specified	Uncertain significance (Aug 30, 2022)
22-46257501-C-T		not specified	Uncertain significance (Nov 08, 2022)
22-46257528-G-A		not specified	Uncertain significance (Jul 12, 2023)
22-46257596-C-G		not specified	Uncertain significance (Mar 16, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PKDREJ	protein_coding	protein_coding	ENST00000253255	1	7660

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.01e-9	0.425	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.03	1037	1.13e+3	0.914	0.0000618	14737
Missense in Polyphen		263	317.21	0.82912		4351
Synonymous	1.18	421	453	0.929	0.0000271	4566
Loss of Function	0.983	16	20.8	0.768	0.00000106	275

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May have a central role in fertilization. May generate a Ca(2+) transporting channel directly involved in initiating the acrosome reaction of the sperm.

Recessive Scores

• pRec: 0.215

Intolerance Scores

• loftool: 0.991
• rvis_EVS: -0.59
• rvis_percentile_EVS: 18.22

Haploinsufficiency Scores

• pHI: 0.0718
• hipred: N
• hipred_score: 0.247

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0463

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pkdrej
• Phenotype: reproductive system phenotype; normal phenotype

Gene ontology

• Biological process: acrosome reaction;detection of mechanical stimulus;calcium ion transmembrane transport
• Cellular component: membrane;integral component of membrane
• Molecular function: calcium channel activity;calcium ion binding