PDXDC1

pyridoxal dependent decarboxylase domain containing 1

Basic information

Region (hg38): 16:14974590-15139339

Links

ENSG00000179889 ∙ NCBI:23042 ∙ OMIM:614244 ∙ HGNC:28995 ∙ Uniprot:Q6P996 ∙ 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 PDXDC1 gene.

• Inborn genetic diseases (58 variants)
• not provided (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDXDC1 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			26	3	3	32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			31	2	1	34
Total	0	0	57	6	4

Variants in PDXDC1

This is a list of pathogenic ClinVar variants found in the PDXDC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-15001816-C-T		not specified	Uncertain significance (Nov 17, 2023)
16-15004190-C-G			Benign (Jun 07, 2017)
16-15004194-A-G		not specified	Uncertain significance (Aug 13, 2021)
16-15004210-G-A		not specified	Uncertain significance (Sep 17, 2021)
16-15004255-C-T		not specified	Uncertain significance (Sep 26, 2023)
16-15006545-G-T		not specified	Uncertain significance (Dec 20, 2023)
16-15008813-C-A			Benign (Aug 03, 2017)
16-15009718-T-C		not specified	Uncertain significance (Jan 03, 2024)
16-15016150-C-T		not specified	Uncertain significance (Aug 10, 2023)
16-15016220-C-T			Benign (Jun 07, 2017)
16-15017324-G-A		not specified	Uncertain significance (Oct 06, 2021)
16-15017374-G-A			Likely benign (Aug 01, 2023)
16-15017388-C-T		Inborn genetic diseases	Uncertain significance (Dec 13, 2021)
16-15017393-A-G			Uncertain significance (Apr 01, 2022)
16-15018844-T-C		not specified	Uncertain significance (Dec 28, 2022)
16-15018915-T-C		not specified	Uncertain significance (Aug 08, 2023)
16-15026668-T-C		not specified	Uncertain significance (May 08, 2023)
16-15028881-C-T		not specified	Uncertain significance (Oct 10, 2023)
16-15028888-T-A		not specified	Likely benign (Dec 13, 2021)
16-15028951-C-G		not specified	Uncertain significance (Jun 02, 2023)
16-15029963-C-G		not specified	Uncertain significance (Jan 23, 2023)
16-15030044-A-G		not specified	Uncertain significance (Jun 03, 2022)
16-15031770-G-A		PDXDC1-related disorder	Likely benign (Mar 31, 2022)
16-15031819-T-C		not specified	Uncertain significance (Apr 11, 2023)
16-15032871-G-A		not specified	Uncertain significance (Sep 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDXDC1	protein_coding	protein_coding	ENST00000396410	23	164749

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.46e-12	0.977	124776	0	972	125748	0.00387

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.466	397	424	0.936	0.0000233	4977
Missense in Polyphen		79	115.15	0.68609		1389
Synonymous	-0.564	176	167	1.06	0.0000102	1472
Loss of Function	2.35	25	41.3	0.605	0.00000189	538

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00246	0.00244
Ashkenazi Jewish	0.00	0.00
East Asian	0.0465	0.0468
Finnish	0.000280	0.000277
European (Non-Finnish)	0.000317	0.000316
Middle Eastern	0.0465	0.0468
South Asian	0.00115	0.00114
Other	0.00131	0.00130

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0996

Intolerance Scores

• loftool: 0.869
• rvis_EVS: 1.38
• rvis_percentile_EVS: 94.63

Haploinsufficiency Scores

• pHI: 0.324
• hipred: N
• hipred_score: 0.492
• ghis: 0.449

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.641

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pdxdc1

Gene ontology

• Biological process: ameboidal-type cell migration;sphingolipid metabolic process;carboxylic acid metabolic process;sphingolipid catabolic process
• Cellular component: endoplasmic reticulum;Golgi apparatus;intracellular membrane-bounded organelle
• Molecular function: sphinganine-1-phosphate aldolase activity;carboxy-lyase activity;pyridoxal phosphate binding;cadherin binding