PDCL

phosducin like

Basic information

Region (hg38): 9:122798389-122828588

Links

ENSG00000136940 ∙ NCBI:5082 ∙ OMIM:604421 ∙ HGNC:8770 ∙ Uniprot:Q13371 ∙ 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 PDCL gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDCL 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					1	1
missense			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	1

Variants in PDCL

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

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

Position	Type	Phenotype	Significance	ClinVar
9-122800155-C-G		not specified	Uncertain significance (Feb 07, 2023)
9-122800176-G-A			Likely benign (Jun 01, 2022)
9-122800199-G-A		not specified	Uncertain significance (Jan 17, 2024)
9-122800219-T-G		not specified	Uncertain significance (Apr 25, 2023)
9-122800258-A-G		not specified	Uncertain significance (Sep 12, 2023)
9-122800302-G-A		not specified	Uncertain significance (Feb 01, 2023)
9-122800346-C-T		not specified	Uncertain significance (Oct 10, 2023)
9-122800351-G-A		not specified	Uncertain significance (Dec 09, 2023)
9-122800535-C-T		not specified	Uncertain significance (Apr 07, 2023)
9-122800537-C-T		not specified	Uncertain significance (May 24, 2023)
9-122800558-G-A		not specified	Uncertain significance (Aug 02, 2023)
9-122800612-A-G		not specified	Uncertain significance (Mar 17, 2023)
9-122800619-G-A		not specified	Likely benign (May 10, 2024)
9-122800727-C-A		not specified	Uncertain significance (Jul 26, 2022)
9-122800729-G-A		not specified	Uncertain significance (May 31, 2024)
9-122800750-A-T		not specified	Uncertain significance (Dec 13, 2023)
9-122800771-G-A		not specified	Uncertain significance (Apr 25, 2022)
9-122800828-C-G		not specified	Uncertain significance (Oct 25, 2022)
9-122800921-C-A		not specified	Uncertain significance (Feb 28, 2024)
9-122800921-C-T		not specified	Uncertain significance (Jul 19, 2023)
9-122800924-G-A		not specified	Uncertain significance (Mar 11, 2022)
9-122800940-G-C		not specified	Uncertain significance (Jul 19, 2022)
9-122800945-G-C		not specified	Uncertain significance (Oct 14, 2021)
9-122800973-C-T		not specified	Uncertain significance (Oct 26, 2022)
9-122800999-C-T		not specified	Uncertain significance (Oct 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDCL	protein_coding	protein_coding	ENST00000259467	3	30243

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.305	0.692	125739	0	7	125746	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.12	131	172	0.761	0.00000927	2028
Missense in Polyphen		39	73.338	0.53178		874
Synonymous	1.25	52	64.8	0.802	0.00000351	539
Loss of Function	2.50	3	12.6	0.238	7.03e-7	142

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000149	0.000148
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a positive regulator of hedgehog signaling and regulates ciliary function. {ECO:0000250|UniProtKB:Q9DBX2}.; FUNCTION: Isoform 2: Acts as a negative regulator of heterotrimeric G proteins assembly by trapping the preloaded G beta subunits inside the CCT chaperonin.
• Pathway: Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding;Metabolism of proteins;Chaperonin-mediated protein folding;Protein folding (Consensus)

Recessive Scores

• pRec: 0.123

Intolerance Scores

• loftool: 0.346
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.32

Haploinsufficiency Scores

• pHI: 0.100
• hipred: Y
• hipred_score: 0.554
• ghis: 0.625

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0868

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pdcl
• Phenotype: homeostasis/metabolism phenotype; vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: protein folding;signal transduction;visual perception;regulation of G protein-coupled receptor signaling pathway;cell projection organization;positive regulation of smoothened signaling pathway;negative regulation of protein refolding;heterotrimeric G-protein complex assembly
• Cellular component: cytoplasm;cytosol;cilium
• Molecular function: protein binding;protein-containing complex binding