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

No genCC data.

ClinVar

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

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.

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			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	0

Variants in PDCL3

This is a list of pathogenic ClinVar variants found in the PDCL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-100566511-C-G		not specified	Uncertain significance (May 08, 2024)
2-100566516-A-G		not specified	Uncertain significance (Aug 12, 2021)
2-100566561-C-G		not specified	Uncertain significance (Apr 05, 2023)
2-100566561-C-T		not specified	Uncertain significance (Nov 09, 2024)
2-100568934-A-G		not specified	Uncertain significance (Aug 10, 2024)
2-100568935-A-T		not specified	Uncertain significance (May 06, 2024)
2-100568981-G-A		not specified	Uncertain significance (Jan 02, 2024)
2-100569627-G-A		not specified	Uncertain significance (Jul 14, 2024)
2-100569633-G-A		not specified	Uncertain significance (Dec 22, 2023)
2-100569682-G-T		not specified	Uncertain significance (Mar 08, 2025)
2-100571624-A-C		not specified	Uncertain significance (Apr 25, 2022)
2-100571691-A-G		not specified	Uncertain significance (Feb 03, 2022)
2-100571715-C-T		not specified	Uncertain significance (May 01, 2024)
2-100571787-T-C		not specified	Uncertain significance (Nov 09, 2024)
2-100576381-G-A		not specified	Uncertain significance (Oct 25, 2024)
2-100576420-C-T		not specified	Uncertain significance (Jul 05, 2024)
2-100576423-T-C		not specified	Uncertain significance (Dec 21, 2023)
2-100576449-C-T		not specified	Uncertain significance (Aug 01, 2022)
2-100576450-G-A		not specified	Uncertain significance (Aug 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDCL3	protein_coding	protein_coding	ENST00000264254	6	14046

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000823	0.533	125719	0	29	125748	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.450	152	137	1.11	0.00000780	1563
Missense in Polyphen		30	36.187	0.82903		465
Synonymous	0.280	45	47.5	0.948	0.00000257	426
Loss of Function	0.711	9	11.6	0.775	4.89e-7	154

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000366	0.000365
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.000111	0.000109
South Asian	0.000163	0.000163
Other	0.000328	0.000326

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

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

Mouse Genome Informatics

• Gene name: Pdcl3

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