PKD2L2

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

Basic information

Region (hg38): 5:137887968-137942747

Links

ENSG00000078795 ∙ NCBI:27039 ∙ OMIM:604669 ∙ HGNC:9012 ∙ Uniprot:Q9NZM6 ∙ 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 PKD2L2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PKD2L2 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						0
missense			41	2		43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3			3
Total	0	0	44	2	0

Variants in PKD2L2

This is a list of pathogenic ClinVar variants found in the PKD2L2 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-137889514-A-G		not specified	Uncertain significance (Jan 19, 2024)
5-137890493-A-G		not specified	Uncertain significance (May 24, 2023)
5-137890500-G-T		not specified	Uncertain significance (Aug 11, 2024)
5-137890532-C-T		not specified	Uncertain significance (Dec 13, 2021)
5-137890543-T-G		not specified	Uncertain significance (Mar 06, 2023)
5-137890577-G-A		not specified	Uncertain significance (Aug 09, 2021)
5-137892480-T-C		not specified	Uncertain significance (Jan 15, 2025)
5-137892492-T-A		not specified	Uncertain significance (Feb 05, 2025)
5-137892493-G-T		not specified	Uncertain significance (Feb 06, 2025)
5-137894368-C-T		not specified	Uncertain significance (Jun 22, 2024)
5-137894438-G-A		not specified	Uncertain significance (Jan 09, 2024)
5-137894444-A-G		not specified	Uncertain significance (Jan 10, 2022)
5-137894502-C-G		not specified	Uncertain significance (Jan 10, 2023)
5-137894537-T-C		not specified	Uncertain significance (Aug 02, 2023)
5-137894538-G-A		not specified	Uncertain significance (Jan 27, 2025)
5-137899697-T-C		not specified	Uncertain significance (Feb 21, 2025)
5-137906240-C-A		not specified	Uncertain significance (Dec 06, 2021)
5-137906252-C-G		not specified	Uncertain significance (Jan 19, 2024)
5-137906282-G-A		not specified	Uncertain significance (Sep 28, 2023)
5-137906318-A-G		not specified	Uncertain significance (Mar 04, 2025)
5-137906343-T-C		not specified	Uncertain significance (Jul 31, 2024)
5-137906371-A-G		not specified	Uncertain significance (May 31, 2023)
5-137906414-C-G		not specified	Uncertain significance (Nov 06, 2023)
5-137906426-C-T		not specified	Uncertain significance (May 22, 2023)
5-137906433-T-C		not specified	Uncertain significance (Oct 11, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PKD2L2	protein_coding	protein_coding	ENST00000290431	14	54780

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.65e-14	0.594	124977	0	237	125214	0.000947

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.18	246	304	0.809	0.0000148	4047
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00110	0.00107
Ashkenazi Jewish	0.00	0.00
East Asian	0.00184	0.00180
Finnish	0.000140	0.000139
European (Non-Finnish)	0.00138	0.00134
Middle Eastern	0.00184	0.00180
South Asian	0.000735	0.000719
Other	0.000844	0.000822

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.372
• hipred: N
• hipred_score: 0.465
• ghis: 0.397

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.123

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pkd2l2
• Phenotype: homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: biological_process;detection of mechanical stimulus;calcium ion transmembrane transport
• Cellular component: membrane;integral component of membrane
• Molecular function: calcium channel activity;calcium ion binding