PDC

phosducin

Basic information

Region (hg38): 1:186443566-186461114

Links

ENSG00000116703 ∙ NCBI:5132 ∙ OMIM:171490 ∙ HGNC:8759 ∙ Uniprot:P20941 ∙ 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 PDC gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDC 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	1

Variants in PDC

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

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

Position	Type	Phenotype	Significance	ClinVar
1-186443996-C-G		not specified	Uncertain significance (Nov 21, 2022)
1-186444049-T-C		not specified	Uncertain significance (Apr 08, 2024)
1-186444080-C-G		not specified	Uncertain significance (Jun 24, 2022)
1-186444092-C-T		not specified	Uncertain significance (Aug 01, 2024)
1-186444178-A-G		not specified	Uncertain significance (Oct 06, 2021)
1-186444181-C-T		not specified	Uncertain significance (Dec 21, 2022)
1-186444229-A-G		not specified	Uncertain significance (Oct 12, 2024)
1-186444239-C-T		not specified	Uncertain significance (Oct 21, 2024)
1-186444292-T-A		not specified	Uncertain significance (Oct 06, 2024)
1-186444292-T-G		not specified	Uncertain significance (Oct 06, 2023)
1-186444312-A-C		not specified	Uncertain significance (Jan 08, 2024)
1-186444346-T-C		not specified	Uncertain significance (Jul 10, 2024)
1-186444449-G-A		not specified	Uncertain significance (Oct 04, 2024)
1-186444462-A-G			Benign (Dec 13, 2017)
1-186444505-A-G		not specified	Uncertain significance (Dec 14, 2021)
1-186446532-C-T		not specified	Uncertain significance (Jun 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDC	protein_coding	protein_coding	ENST00000391997	3	17557

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000101	0.594	125679	0	47	125726	0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.603	107	126	0.849	0.00000606	1644
Missense in Polyphen		30	33.642	0.89175		428
Synonymous	1.55	30	42.9	0.699	0.00000194	435
Loss of Function	0.676	7	9.22	0.760	4.87e-7	122

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000363	0.000363
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000547	0.0000544
Finnish	0.000971	0.000971
European (Non-Finnish)	0.0000969	0.0000967
Middle Eastern	0.0000547	0.0000544
South Asian	0.000164	0.000163
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May participate in the regulation of visual phototransduction or in the integration of photoreceptor metabolism. Inhibits the transcriptional activation activity of the cone-rod homeobox CRX. {ECO:0000269|PubMed:10866677}.

Recessive Scores

• pRec: 0.478

Intolerance Scores

• loftool: 0.857
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.12

Haploinsufficiency Scores

• pHI: 0.168
• hipred: N
• hipred_score: 0.383
• ghis: 0.433

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.882

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pdc
• Phenotype: renal/urinary system 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); vision/eye phenotype; 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); homeostasis/metabolism phenotype; muscle phenotype

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;visual perception;phototransduction;negative regulation of catalytic activity
• Cellular component: photoreceptor outer segment;photoreceptor inner segment;nucleus;cytosol
• Molecular function: phospholipase inhibitor activity