PDXDC1

pyridoxal dependent decarboxylase domain containing 1

Basic information

Region (hg38): 16:14974591-15153671

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.

• not_specified (104 variants)
• PDXDC1-related_disorder (8 variants)
• not_provided (5 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. These statistics are base on transcript: NM_000015027.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				4		4
missense			101	7	1	109
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	101	11	1

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