PKD2L1
polycystin 2 like 1, transient receptor potential cation channel, the group of Transient receptor potential cation channels
Basic information
Region (hg38): 10:100288149-100330264
Previous symbols: [ "PKD2L", "PKDL" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (104 variants)
- not_provided (15 variants)
- Prostate_cancer (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PKD2L1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000016112.3. 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 | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 6 | |||||
| missense | 98 | 110 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 98 | 9 | 9 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PKD2L1 | protein_coding | protein_coding | ENST00000318222 | 16 | 42341 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.57e-27 | 0.000289 | 122437 | 230 | 3081 | 125748 | 0.0133 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.0696 | 450 | 454 | 0.991 | 0.0000252 | 5255 |
| Missense in Polyphen | 167 | 167.73 | 0.99566 | 2080 | ||
| Synonymous | -0.855 | 199 | 184 | 1.08 | 0.0000105 | 1571 |
| Loss of Function | 0.213 | 42 | 43.5 | 0.965 | 0.00000238 | 457 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.192 | 0.186 |
| Ashkenazi Jewish | 0.00232 | 0.00228 |
| East Asian | 0.00159 | 0.00158 |
| Finnish | 0.000418 | 0.000416 |
| European (Non-Finnish) | 0.00159 | 0.00156 |
| Middle Eastern | 0.00159 | 0.00158 |
| South Asian | 0.00176 | 0.00170 |
| Other | 0.00990 | 0.00916 |
dbNSFP
Source:
- Function
- FUNCTION: Pore-forming subunit of a ciliary calcium channel that controls calcium concentration within primary cilia without affecting cytoplasmic calcium concentration. Forms a heterodimer with PKD1L1 in primary cilia and forms a calcium-permeant ciliary channel that regulates sonic hedgehog/SHH signaling and GLI2 transcription. May act as a sour taste receptor by forming a calcium channel with PKD1L3 in gustatory cells; however, its contribution to sour taste perception is unclear in vivo and may be indirect. {ECO:0000269|PubMed:10517637, ECO:0000269|PubMed:19812697, ECO:0000269|PubMed:23212381, ECO:0000269|PubMed:24336289}.;
- Pathway
- Taste transduction - Homo sapiens (human)
(Consensus)
Recessive Scores
- pRec
- 0.120
Intolerance Scores
- loftool
- 0.632
- rvis_EVS
- 1.01
- rvis_percentile_EVS
- 90.8
Haploinsufficiency Scores
- pHI
- 0.453
- hipred
- N
- hipred_score
- 0.251
- ghis
- 0.388
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.575
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pkd2l1
- Phenotype
- nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); taste/olfaction phenotype;
Zebrafish Information Network
- Gene name
- pkd2l1
- Affected structure
- Kolmer-Agduhr neuron
- Phenotype tag
- abnormal
- Phenotype quality
- decreased process quality
Gene ontology
- Biological process
- detection of chemical stimulus involved in sensory perception of sour taste;cation transport;smoothened signaling pathway;response to water;sodium ion transmembrane transport;detection of chemical stimulus involved in sensory perception of taste;sensory perception of sour taste;detection of mechanical stimulus;protein homotetramerization;calcium ion transmembrane transport;cellular response to acidic pH;potassium ion transmembrane transport;inorganic cation transmembrane transport
- Cellular component
- endoplasmic reticulum;plasma membrane;integral component of plasma membrane;cell surface;membrane;integral component of membrane;calcium channel complex;intracellular membrane-bounded organelle;receptor complex;ciliary membrane;non-motile cilium
- Molecular function
- calcium activated cation channel activity;cation channel activity;calcium channel activity;sodium channel activity;calcium ion binding;protein binding;cytoskeletal protein binding;cation transmembrane transporter activity;calcium-activated potassium channel activity;sour taste receptor activity;identical protein binding;muscle alpha-actinin binding;alpha-actinin binding