PCYT1B
Basic information
Region (hg38): X:24558087-24672677
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCYT1B 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 | 2 | |||||
| missense | 9 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 9 | 2 | 0 |
Variants in PCYT1B
This is a list of pathogenic ClinVar variants found in the PCYT1B region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| X-24562316-C-T | not specified | Uncertain significance (Jan 17, 2025) | ||
| X-24562362-G-A | Likely benign (Feb 01, 2023) | |||
| X-24562409-G-A | not specified | Uncertain significance (Jan 09, 2024) | ||
| X-24562471-A-G | not specified | Uncertain significance (Dec 07, 2024) | ||
| X-24562475-T-G | not specified | Uncertain significance (Apr 04, 2023) | ||
| X-24575238-A-G | Likely benign (Feb 01, 2023) | |||
| X-24590024-T-C | not specified | Uncertain significance (May 27, 2022) | ||
| X-24590028-G-A | not specified | Uncertain significance (Nov 23, 2024) | ||
| X-24590181-C-T | Likely benign (Nov 01, 2023) | |||
| X-24619030-G-T | not specified | Uncertain significance (Nov 15, 2021) | ||
| X-24619040-C-G | not specified | Uncertain significance (Jan 17, 2024) | ||
| X-24647033-C-T | not specified | Uncertain significance (Aug 28, 2024) | ||
| X-24647045-C-T | not specified | Uncertain significance (Jul 19, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PCYT1B | protein_coding | protein_coding | ENST00000379144 | 8 | 114591 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.897 | 0.103 | 125701 | 1 | 1 | 125703 | 0.00000796 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.16 | 65 | 136 | 0.479 | 0.0000107 | 2424 |
| Missense in 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 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000256 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Controls phosphatidylcholine synthesis.;
- Pathway
- 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;Metabolism of lipids;phosphatidylcholine biosynthesis;Metabolism;Synthesis of PC;Glycerophospholipid metabolism;Glycerophospholipid biosynthesis;Phospholipid metabolism
(Consensus)
Recessive Scores
- pRec
- 0.134
Intolerance Scores
- loftool
- 0.0434
- rvis_EVS
- -0.05
- rvis_percentile_EVS
- 49.76
Haploinsufficiency Scores
- pHI
- 0.194
- hipred
- Y
- hipred_score
- 0.728
- ghis
- 0.690
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.984
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pcyt1b
- Phenotype
- neoplasm; reproductive system phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype;
Gene ontology
- Biological process
- ovarian follicle development;phosphatidylcholine biosynthetic process;CDP-choline pathway;spermatogenesis
- Cellular component
- cytoplasm;endoplasmic reticulum membrane
- Molecular function
- choline-phosphate cytidylyltransferase activity;phosphatidylcholine binding