PCBD2
protein-codingpterin-4 alpha-carbinolamine dehydratase 2, the group of MicroRNA protein coding host genes
Gene summary
Predicted to enable 4-alpha-hydroxytetrahydrobiopterin dehydratase activity; identical protein binding activity; and phenylalanine 4-monooxygenase activity. Involved in positive regulation of DNA-templated transcription. Located in mitochondrion. [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 ~102.8 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 PCBD2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_032151.5. 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 | 0 | |||||
| missense | 22 | 2 | 24 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 22 | 2 | 0 | 24 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_115527.3 | 4 | MANE Select | |
| Ensembl | ENSP00000254908.6 | 4 | MANE Select | |
| Ensembl | ENSP00000426161.1 | 4 | Standard | |
| Ensembl | ENSP00000421544.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Folate biosynthesis - Homo sapiens (human)
- phenylalanine degradation/tyrosine biosynthesis
- Biopterin metabolism
Biological Process
- tetrahydrobiopterin biosynthetic process
- positive regulation of transcription, DNA-templated
- protein homotetramerization
- protein heterooligomerization
- oxidation-reduction process
Molecular Function
- phenylalanine 4-monooxygenase activity
- protein binding
- 4-alpha-hydroxytetrahydrobiopterin dehydratase activity
Cellular Component
- cellular_component
- nucleus
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000512783
- Coding exons
- 4
- Length
- 103054
- Individuals with no LoFs
- 124787
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 4
- Defined
- 124791
- p
- 0.0000160
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.179 | 48 | 51.6 | 0.930 | 0.00000229 | 839 |
| Missense (PolyPhen) | 23 | 24.803 | 0.92732 | 341 | ||
| Synonymous | -0.944 | 23 | 17.9 | 1.28 | 8.58e-7 | 256 |
| Loss of Function | 1.02 | 3 | 5.62 | 0.534 | 2.37e-7 | 81 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000065 | 0.000065 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000056 | 0.000056 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000018 | 0.000018 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Involved in tetrahydrobiopterin biosynthesis. Seems to both prevent the formation of 7-pterins and accelerate the formation of quinonoid-BH2 (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.0987
Intolerance Scores
- LoFtool
- 0.664
- RVIS EVS
- 0.08
- RVIS percentile EVS
- 59.43
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.855
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Medium |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Medium | Medium |