GeneBe

PKD1L1

polycystin 1 like 1, transient receptor potential channel interacting

Basic information

Region (hg38): 7:47740202-47948466

Links

ENSG00000158683 ∙ NCBI:168507 ∙ OMIM:609721 ∙ HGNC:18053 ∙ Uniprot:Q8TDX9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • heterotaxy, visceral, 8, autosomal (Strong), mode of inheritance: AR
  • heterotaxy, visceral, 8, autosomal (Moderate), mode of inheritance: AR
  • situs inversus (Supportive), mode of inheritance: AD
  • heterotaxy, visceral, 8, autosomal (Strong), mode of inheritance: AR
  • heterotaxy, visceral, 8, autosomal (Definitive), mode of inheritance: AR
  • heterotaxy, visceral, 8, autosomal (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Heterotaxy, visceral, 8, autosomalARCardiovascularThe condition can involve congenital cardiac anomalies, and awareness may allow early managementCardiovascular; Gastrointestinal; Renal27616478
The ocndition can include multiple congenital anomalies

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PKD1L1 gene.

  • Inborn_genetic_diseases (411 variants)
  • not_provided (358 variants)
  • PKD1L1-related_disorder (267 variants)
  • Heterotaxy,_visceral,_8,_autosomal (66 variants)
  • not_specified (9 variants)
  • Situs_inversus (3 variants)
  • Congenital_chylothorax (3 variants)
  • EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)
  • Autism (1 variants)
  • Heterotaxy (1 variants)
  • Visceral_heterotaxy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PKD1L1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000138295.5. 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.

EffectPLPVUSLBBSum
synonymous
8
clinvar
155
clinvar
24
clinvar
 187
missense
2
clinvar
459
clinvar
75
clinvar
23
clinvar
 559
nonsense
12
clinvar
10
clinvar
 22
start loss
0
frameshift
9
clinvar
14
clinvar
1
clinvar
 24
splice donor/acceptor (+/-2bp)
1
clinvar
11
clinvar
3
clinvar
 15
Total 22 37 471 230 47

Highest pathogenic variant AF is 0.0008608

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PKD1L1protein_codingprotein_codingENST00000289672 57173839
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
1.09e-401.0012535903891257480.00155
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.33515121.55e+30.9760.000084718505
Missense in Polyphen267326.230.818454326
Synonymous-0.5856376181.030.00003645730
Loss of Function4.29881440.6130.000007411636

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.002820.00275
Ashkenazi Jewish0.0008090.000794
East Asian0.0009390.000925
Finnish0.0009750.000971
European (Non-Finnish)0.002000.00194
Middle Eastern0.0009390.000925
South Asian0.001460.00144
Other0.001490.00147

dbNSFP

Source: dbNSFP

Function
FUNCTION: Component of a ciliary calcium channel that controls calcium concentration within primary cilia without affecting cytoplasmic calcium concentration. Forms a heterodimer with PKD2L1 in primary cilia and forms a calcium-permeant ciliary channel that regulates sonic hedgehog/SHH signaling and GLI2 transcription. Does not constitute the pore-forming subunit. Also involved in left/right axis specification downstream of nodal flow: forms a complex with PKD2 in cilia to facilitate flow detection in left/right patterning. {ECO:0000269|PubMed:24336289}.;

Intolerance Scores

loftool
0.921
rvis_EVS
2.17
rvis_percentile_EVS
98.05

Haploinsufficiency Scores

pHI
0.0712
hipred
N
hipred_score
0.233
ghis

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.159

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumHigh
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Pkd1l1
Phenotype
normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); embryo phenotype; respiratory system phenotype; digestive/alimentary phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype;

Gene ontology

Biological process
detection of nodal flow;detection of mechanical stimulus;calcium ion transmembrane transport;left/right axis specification;cell-cell adhesion
Cellular component
cilium;membrane;calcium channel complex;ciliary membrane;non-motile cilium
Molecular function
calcium channel activity;protein binding