PKDREJ

polycystin family receptor for egg jelly

Basic information

Region (hg38): 22:46255663-46263343

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.

• not_specified (303 variants)
• not_provided (4 variants)

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. These statistics are base on transcript: NM_000006071.2. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				4		4
missense			276	27		303
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	276	31	0

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