PKD2L2

protein-coding

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

Gene summary

Predicted to enable calcium channel activity. Predicted to be involved in detection of mechanical stimulus. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001300921.2

Inheritance

—

ClinVar variants

U:81B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.71

Max pathogenic AF

—

Genomic locus

chr5:137,887,968-137,942,747

External References & Databases

Ensembl (ENSG00000078795)

Transcript & Mutation Effects

hg38 • Region Span ~54.8 kb

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GenCC 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 PKD2L2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 88

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001300921.2. 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						0
missense			80 clinvar	3 clinvar		83
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	81	3	0	84

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 19 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001300921.2	RefSeq	NP_001287850.1	14	MANE Select
ENST00000508883.6	Ensembl	ENSP00000424725.1	14	MANE Select
NM_001258448.2	RefSeq	NP_001245377.1	14	Standard
NM_001258449.2	RefSeq	NP_001245378.1	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biological_process
detection of mechanical stimulus
calcium ion transmembrane transport

Molecular Function

calcium channel activity
calcium ion binding

Cellular Component

membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000290431
Coding exons: 14
Length: 54780
Individuals with no LoFs: 124977
Homozygous LoFs: 0
Heterozygous LoFs: 237
Defined: 125214
p: 0.000947

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.18	246	304	0.809	0.0000148	4047
Missense (PolyPhen)		85	104.21	0.81565		1476
Synonymous	1.17	88	103	0.853	0.00000498	1067
Loss of Function	1.61	26	36.5	0.713	0.00000197	446

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00079	0.00077	rare
Latino/Admixed American	0.00030	0.00029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0018	0.0018	notable
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.0014	0.0013	notable
South Asian	0.00074	0.00072	rare
Other	0.00084	0.00082	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May function as a subunit of a cation channel and play a role in fertilization.;

Recessive Scores

pRec: 0.104

Intolerance Scores

LoFtool: 0.893
RVIS EVS: -0.22
RVIS percentile EVS: 37.54

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.123

Gene Damage Prediction

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