GeneBe

PDCL3

phosducin like 3

Basic information

Region (hg38): 2:100562993-100577472

Links

ENSG00000115539 ∙ NCBI:79031 ∙ OMIM:611678 ∙ HGNC:28860 ∙ Uniprot:Q9H2J4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • megacystis-microcolon-intestinal hypoperistalsis syndrome (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PDCL3 gene.

  • not_specified (30 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDCL3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000024065.5. 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
0
missense
28
clinvar
2
clinvar
 30
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 28 2 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PDCL3protein_codingprotein_codingENST00000264254 614046
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.000008230.5331257190291257480.000115
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.4501521371.110.000007801563
Missense in Polyphen3036.1870.82903465
Synonymous0.2804547.50.9480.00000257426
Loss of Function0.711911.60.7754.89e-7154

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003660.000365
Ashkenazi Jewish0.000.00
East Asian0.0001110.000109
Finnish0.000.00
European (Non-Finnish)0.0001060.000105
Middle Eastern0.0001110.000109
South Asian0.0001630.000163
Other0.0003280.000326

dbNSFP

Source: dbNSFP

Function
FUNCTION: Acts as a chaperone for the angiogenic VEGF receptor KDR/VEGFR2, controlling its abundance and inhibiting its ubiquitination and degradation. Modulates the activation of caspases during apoptosis. Is a substrate for Orgyia pseudotsugata multicapsid polyhedrosis virus (OpMNPV) IAP-mediated ubiquitination. {ECO:0000269|PubMed:15371430, ECO:0000269|PubMed:23792958}.;

Recessive Scores

pRec
0.0925

Intolerance Scores

loftool
0.821
rvis_EVS
0.02
rvis_percentile_EVS
55.22

Haploinsufficiency Scores

pHI
0.0999
hipred
N
hipred_score
0.251
ghis
0.476

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
K
gene_indispensability_pred
N
gene_indispensability_score
0.364

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Pdcl3
Phenotype

Zebrafish Information Network

Gene name
pdcl3
Affected structure
intersegmental vessel
Phenotype tag
abnormal
Phenotype quality
decreased length

Gene ontology

Biological process
angiogenesis;positive regulation of endothelial cell proliferation;protein folding;apoptotic process;viral process;positive regulation of angiogenesis;regulation of peptidyl-tyrosine phosphorylation;negative regulation of ubiquitin-dependent protein catabolic process
Cellular component
nucleus;cytoplasm;cytosol
Molecular function
protein binding;vascular endothelial growth factor receptor 2 binding;protein folding chaperone