PPCDC

phosphopantothenoylcysteine decarboxylase

Basic information

Region (hg38): 15:75023585-75117462

Links

ENSG00000138621 ∙ NCBI:60490 ∙ OMIM:609854 ∙ HGNC:28107 ∙ Uniprot:Q96CD2 ∙ 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 PPCDC gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPCDC 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				2	1	3
missense			11	1		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			1		1	2
Total	0	0	12	3	2

Variants in PPCDC

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

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

Position	Type	Phenotype	Significance	ClinVar
15-75028349-G-C		not specified	Uncertain significance (Mar 20, 2024)
15-75028384-G-T			Benign (Jun 10, 2018)
15-75043492-C-A		not specified	Uncertain significance (Mar 25, 2024)
15-75043516-A-C		not specified	Uncertain significance (Sep 29, 2023)
15-75043519-G-A		not specified	Uncertain significance (May 17, 2023)
15-75043523-C-A		not specified	Uncertain significance (Feb 16, 2023)
15-75043531-T-C		not specified	Uncertain significance (Jan 31, 2023)
15-75043533-G-C		not specified	Uncertain significance (Jun 29, 2023)
15-75044388-A-G			Benign (Mar 26, 2019)
15-75044412-T-A			Likely benign (May 30, 2018)
15-75048559-G-A		not specified	Likely benign (Feb 11, 2022)
15-75048565-C-T		not specified	Uncertain significance (Jun 22, 2021)
15-75048577-C-G		not specified	Uncertain significance (Jun 24, 2022)
15-75048593-T-C		not specified	Uncertain significance (Apr 05, 2023)
15-75048602-C-T		not specified	Uncertain significance (Jan 31, 2022)
15-75048644-A-G		not specified	Uncertain significance (Jun 27, 2022)
15-75048706-G-A		not specified	Uncertain significance (May 09, 2024)
15-75048706-G-C		not specified	Uncertain significance (Mar 27, 2023)
15-75049142-G-C			Likely benign (Jun 13, 2018)
15-75049181-C-T			Likely benign (Oct 30, 2018)
15-75049182-G-A		not specified	Uncertain significance (Jan 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPCDC	protein_coding	protein_coding	ENST00000342932	5	93908

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000479	0.690	125727	0	19	125746	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.430	110	123	0.891	0.00000700	1332
Missense in Polyphen		36	45.24	0.79576		451
Synonymous	0.937	41	49.4	0.830	0.00000310	403
Loss of Function	0.811	6	8.56	0.701	3.62e-7	102

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000120
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.0000969	0.0000967
Middle Eastern	0.000272	0.000272
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Necessary for the biosynthesis of coenzyme A. Catalyzes the decarboxylation of 4-phosphopantothenoylcysteine to form 4'- phosphopantotheine. {ECO:0000269|PubMed:11923312, ECO:0000269|PubMed:15581364}.
• Pathway: Pantothenate and CoA biosynthesis - Homo sapiens (human);Pantothenate and CoA Biosynthesis;Coenzyme A biosynthesis;Metabolism;Vitamin B5 (pantothenate) metabolism;Metabolism of water-soluble vitamins and cofactors;Metabolism of vitamins and cofactors;coenzyme A biosynthesis (Consensus)

Recessive Scores

• pRec: 0.136

Intolerance Scores

• loftool: 0.571
• rvis_EVS: -0.12
• rvis_percentile_EVS: 45.13

Haploinsufficiency Scores

• pHI: 0.222
• hipred: N
• hipred_score: 0.350
• ghis: 0.531

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.950

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppcdc

Gene ontology

• Biological process: coenzyme biosynthetic process;coenzyme A biosynthetic process
• Cellular component: cytosol
• Molecular function: phosphopantothenoylcysteine decarboxylase activity;protein binding;identical protein binding