PKD1L2
protein-codingpolycystin 1 like 2 (gene/pseudogene), the group of C-type lectin domain containing
Gene summary
This gene encodes a member of the polycystin protein family. This protein may function as a G-protein-coupled component or regulator of cation channel pores. The long isoform of this protein contains 11 transmembrane domains, a latrophilin/CL-1-like GPCR proteolytic site (GPS) domain, and a polycystin-1, lipoxygenase, alpha-toxin (PLAT) domain. Alternative splicing results in multiple transcript variants encoding distinct isoforms. This gene is a polymorphic pseudogene in humans. [provided by RefSeq, May 2022]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~119.5 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to PKD1L2 variants in ClinVar
No annotated ClinVar phenotypes.
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript . Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 1 | 265 | 19 | 1 | 286 | |
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 1 | 266 | 20 | 1 | 288 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| Ensembl | ENSP00000434417.1 | 43 | Standard | |
| Ensembl | ENSP00000436389.1 | 12 | Standard | |
| Ensembl | ENSP00000432818.1 | 4 | Standard | |
| Ensembl | ENSP00000432818.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- detection of mechanical stimulus
- calcium ion transmembrane transport
Molecular Function
- calcium channel activity
- calcium ion binding
- carbohydrate binding
Cellular Component
- membrane
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- polymorphic_pseudogene
- Transcript type
- protein_coding
- Transcript
- ENST00000527937
- Coding exons
- 4
- Length
- 119496
- Individuals with no LoFs
- 124742
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 53
- Defined
- 124795
- p
- 0.000212
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -3.24 | 237 | 132 | 1.79 | 0.00000695 | 1508 |
| Missense (PolyPhen) | 56 | 32.327 | 1.7323 | 433 | ||
| Synonymous | -1.75 | 72 | 55.4 | 1.30 | 0.00000308 | 511 |
| Loss of Function | -0.0441 | 7 | 6.88 | 1.02 | 3.77e-7 | 72 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0022 | 0.0022 | notable |
| Latino/Admixed American | 0.00012 | 0.00012 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00022 | 0.00022 | rare |
| Finnish | 0.000093 | 0.000093 | rare |
| European (Non-Finnish) | 0.000035 | 0.000035 | rare |
| South Asian | 0.000098 | 0.000098 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May function as an ion-channel regulator. May function as a G-protein-coupled receptor. {ECO:0000269|PubMed:15203210}.;
Recessive Scores
- pRec
- 0.0772
Intolerance Scores
- RVIS EVS
- 6.86
- RVIS percentile EVS
- 99.89
Essentials
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N