PDXDC1
protein-codingpyridoxal dependent decarboxylase domain containing 1
Gene summary
Enables cadherin binding activity. Located in Golgi apparatus. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~179.1 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to PDXDC1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_015027.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | 4 | 7 | |||
| missense | 128 | 8 | 1 | 137 | ||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 8 | 8 | ||||
| Total | 0 | 0 | 141 | 12 | 1 | 154 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_055842.2 | 23 | MANE Select | |
| Ensembl | ENSP00000379691.4 | 23 | MANE Select | |
| RefSeq | NP_001272373.1 | 22 | Standard | |
| RefSeq | NP_001272374.1 | 22 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- ameboidal-type cell migration
- sphingolipid metabolic process
- carboxylic acid metabolic process
- sphingolipid catabolic process
Molecular Function
- sphinganine-1-phosphate aldolase activity
- carboxy-lyase activity
- pyridoxal phosphate binding
- cadherin binding
Cellular Component
- endoplasmic reticulum
- Golgi apparatus
- intracellular membrane-bounded organelle
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000396410
- Coding exons
- 23
- Length
- 164749
- Individuals with no LoFs
- 124776
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 972
- Defined
- 125748
- p
- 0.00387
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.466 | 397 | 424 | 0.936 | 0.0000233 | 4977 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0021 | 0.0020 | notable |
| Latino/Admixed American | 0.00041 | 0.00040 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.046 | 0.047 | notable |
| Finnish | 0.00028 | 0.00028 | rare |
| European (Non-Finnish) | 0.00032 | 0.00032 | rare |
| South Asian | 0.0012 | 0.0011 | notable |
| Other | 0.0013 | 0.0013 | notable |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.0996
Intolerance Scores
- LoFtool
- 0.869
- RVIS EVS
- 1.38
- RVIS percentile EVS
- 94.63
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.641
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |