PKD2L1

polycystin 2 like 1, transient receptor potential cation channel, the group of Transient receptor potential cation channels

Basic information

Region (hg38): 10:100288148-100330264

Previous symbols: [ "PKD2L", "PKDL" ]

Links

ENSG00000107593 ∙ NCBI:9033 ∙ OMIM:604532 ∙ HGNC:9011 ∙ Uniprot:Q9P0L9 ∙ 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 PKD2L1 gene.

• Inborn genetic diseases (25 variants)
• not provided (15 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.

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					5	5
missense			25	2	4	31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	2	3
non coding					1	1
Total	0	0	25	2	10

Variants in PKD2L1

This is a list of pathogenic ClinVar variants found in the PKD2L1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-100288412-G-A		not specified	Likely benign (Dec 07, 2023)
10-100288427-C-T			Benign (Mar 28, 2018)
10-100288434-G-T		not specified	Uncertain significance (Feb 26, 2024)
10-100288437-T-C		not specified	Uncertain significance (Mar 24, 2023)
10-100288980-T-C		not specified	Uncertain significance (Jun 11, 2021)
10-100288990-G-C		not specified	Uncertain significance (Dec 08, 2023)
10-100289008-G-A		not specified	Uncertain significance (Jul 14, 2023)
10-100289031-G-A		not specified	Likely benign (Feb 28, 2024)
10-100290022-G-T		not specified	Uncertain significance (Oct 30, 2023)
10-100290045-C-A		not specified	Uncertain significance (Sep 14, 2022)
10-100290063-C-A		not specified	Uncertain significance (Dec 21, 2023)
10-100290125-C-A		not specified	Uncertain significance (Nov 03, 2023)
10-100290141-G-A			Benign (May 16, 2018)
10-100290500-A-G		not specified	Uncertain significance (Dec 18, 2023)
10-100291335-T-A			Benign (Jun 05, 2018)
10-100291354-T-G		not specified	Uncertain significance (Dec 19, 2023)
10-100291357-G-A			Benign (Feb 09, 2018)
10-100292963-G-A		not specified	Uncertain significance (Dec 23, 2022)
10-100293357-T-C		not specified	Uncertain significance (Aug 02, 2021)
10-100293374-C-A			Likely benign (Jun 05, 2018)
10-100294606-C-A		not specified	Uncertain significance (Nov 27, 2023)
10-100294636-T-G		not specified	Uncertain significance (Nov 08, 2022)
10-100294640-C-T			Benign (Feb 27, 2018)
10-100294952-T-G		not specified	Uncertain significance (Aug 02, 2022)
10-100294982-C-T		not specified	Uncertain significance (Oct 13, 2023)

GnomAD

Source: gnomAD

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: dbNSFP

• 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