PDXDC2P

pyridoxal dependent decarboxylase domain containing 2, pseudogene

Basic information

Region (hg38): 16:70010751-70065776

Previous symbols: [ "PDXDC2" ]

Links

ENSG00000255185 ∙ NCBI:109731405 ∙ ∙ HGNC:27559 ∙ Uniprot:Q6P474 ∙ 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 PDXDC2P gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDXDC2P 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						0
missense						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	0	0

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0896

Haploinsufficiency Scores

• pHI: 0.174

Gene ontology

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