PCYT1B
protein-codingphosphate cytidylyltransferase 1B, choline
Gene summary
The protein encoded by this gene belongs to the cytidylyltransferase family. It is involved in the regulation of phosphatidylcholine biosynthesis. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~114.6 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 PCYT1B variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_004845.5. 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 | 3 | 2 | 5 | |||
| missense | 27 | 27 | ||||
| nonsense | 3 | 3 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 36 | 2 | 0 | 38 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_004836.2 | 8 | MANE Select | |
| Ensembl | ENSP00000368439.2 | 8 | MANE Select | |
| RefSeq | NP_001156736.1 | 8 | Standard | |
| RefSeq | NP_001156737.1 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Glycerophospholipid metabolism - Homo sapiens (human)
- Choline metabolism in cancer - Homo sapiens (human)
- Phosphonate and phosphinate metabolism - Homo sapiens (human)
- Kennedy pathway from Sphingolipids
- One carbon metabolism and related pathways
Biological Process
- ovarian follicle development
- phosphatidylcholine biosynthetic process
- CDP-choline pathway
- spermatogenesis
Molecular Function
- choline-phosphate cytidylyltransferase activity
- phosphatidylcholine binding
Cellular Component
- cytoplasm
- endoplasmic reticulum membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000379144
- Coding exons
- 8
- Length
- 114591
- Individuals with no LoFs
- 125701
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 1
- Defined
- 125703
- p
- 0.00000796
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.16 | 65 | 136 | 0.479 | 0.0000107 | 2424 |
| Missense (PolyPhen) | 11 | 39.73 | 0.27687 | 667 | ||
| Synonymous | -0.499 | 56 | 51.5 | 1.09 | 0.00000424 | 691 |
| Loss of Function | 2.91 | 1 | 11.8 | 0.0850 | 8.18e-7 | 227 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000026 | 0.000018 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Controls phosphatidylcholine synthesis.;
Recessive Scores
- pRec
- 0.134
Intolerance Scores
- LoFtool
- 0.0434
- RVIS EVS
- -0.05
- RVIS percentile EVS
- 49.76
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.984
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |