PKD1L2

polycystin 1 like 2 (gene/pseudogene), the group of C-type lectin domain containing

Basic information

Region (hg38): 16:81100874-81220370

Links

ENSG00000166473 ∙ NCBI:114780 ∙ OMIM:607894 ∙ HGNC:21715 ∙ Uniprot:Q7Z442 ∙ 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 PKD1L2 gene.

• Inborn genetic diseases (152 variants)
• Marfanoid habitus and intellectual disability (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PKD1L2 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			142	10		152
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	143	10	0

Variants in PKD1L2

This is a list of pathogenic ClinVar variants found in the PKD1L2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-81130461-G-T		not specified	Uncertain significance (Sep 23, 2023)
16-81130500-G-A		not specified	Uncertain significance (Nov 30, 2022)
16-81130591-G-A		not specified	Uncertain significance (Oct 12, 2021)
16-81130615-G-T		not specified	Uncertain significance (Jun 18, 2021)
16-81130621-G-C		not specified	Uncertain significance (Dec 19, 2022)
16-81133608-G-T		not specified	Uncertain significance (Jan 18, 2023)
16-81133626-C-T		not specified	Uncertain significance (Sep 27, 2021)
16-81133646-G-A		not specified	Uncertain significance (Mar 07, 2024)
16-81133653-A-G		not specified	Uncertain significance (Oct 17, 2023)
16-81133660-C-A		not specified	Uncertain significance (May 27, 2022)
16-81133663-G-T		not specified	Likely benign (Oct 20, 2021)
16-81137458-G-C		not specified	Uncertain significance (Jul 06, 2021)
16-81137479-C-T		not specified	Uncertain significance (Dec 22, 2023)
16-81137521-C-G		not specified	Uncertain significance (Jan 10, 2023)
16-81139516-G-A		not specified	Uncertain significance (Sep 16, 2021)
16-81139536-T-C		not specified	Uncertain significance (Feb 17, 2023)
16-81139549-C-T		not specified	Uncertain significance (May 23, 2023)
16-81139553-C-T		not specified	Likely benign (Feb 10, 2022)
16-81139583-C-A		not specified	Uncertain significance (Mar 11, 2022)
16-81139597-G-T		not specified	Uncertain significance (Feb 13, 2023)
16-81139599-C-T		not specified	Uncertain significance (Sep 29, 2022)
16-81141306-G-T		not specified	Uncertain significance (Jul 26, 2021)
16-81147397-C-T		not specified	Uncertain significance (Jul 14, 2023)
16-81147400-C-A		not specified	Uncertain significance (Feb 06, 2024)
16-81147409-A-C		not specified	Uncertain significance (May 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PKD1L2	polymorphic_pseudogene	protein_coding	ENST00000527937	4	119496

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000209	0.294	124742	0	53	124795	0.000212

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-3.24	237	132	1.79	0.00000695	1508
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00231	0.00231
Ashkenazi Jewish	0.00	0.00
East Asian	0.000222	0.000223
Finnish	0.0000928	0.0000928
European (Non-Finnish)	0.0000353	0.0000353
Middle Eastern	0.000222	0.000223
South Asian	0.0000981	0.0000980
Other	0.000330	0.000330

dbNSFP

Source: dbNSFP

• 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

Haploinsufficiency Scores

• pHI: 0.0964
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Pkd1l2
• Phenotype: reproductive system phenotype; vision/eye phenotype

Gene ontology

• 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;carbohydrate binding