PCM1
pericentriolar material 1
Basic information
Region (hg38): 8:17922842-18029948
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (368 variants)
- not_provided (29 variants)
- PCM1-related_disorder (10 variants)
- EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)
- Thyroid_cancer,_nonmedullary,_1 (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCM1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006197.4. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 10 | 15 | ||||
| missense | 360 | 23 | 385 | |||
| nonsense | 3 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 362 | 34 | 7 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PCM1 | protein_coding | protein_coding | ENST00000325083 | 37 | 105130 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 3.71e-16 | 1.00 | 124562 | 1 | 92 | 124655 | 0.000373 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -6.16 | 1474 | 942 | 1.56 | 0.0000467 | 13318 |
| Missense in Polyphen | 497 | 352.83 | 1.4086 | 5218 | ||
| Synonymous | -7.26 | 491 | 325 | 1.51 | 0.0000164 | 3568 |
| Loss of Function | 5.02 | 43 | 96.1 | 0.447 | 0.00000476 | 1314 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000972 | 0.000955 |
| Ashkenazi Jewish | 0.000301 | 0.000298 |
| East Asian | 0.000235 | 0.000223 |
| Finnish | 0.000423 | 0.000418 |
| European (Non-Finnish) | 0.000364 | 0.000345 |
| Middle Eastern | 0.000235 | 0.000223 |
| South Asian | 0.000482 | 0.000458 |
| Other | 0.000178 | 0.000165 |
dbNSFP
Source:
- Function
- FUNCTION: Required for centrosome assembly and function (PubMed:12403812, PubMed:15659651, PubMed:16943179). Essential for the correct localization of several centrosomal proteins including CEP250, CETN3, PCNT and NEK2 (PubMed:12403812, PubMed:15659651). Required to anchor microtubules to the centrosome (PubMed:12403812, PubMed:15659651). Involved in the biogenesis of cilia (PubMed:20551181, PubMed:24121310). {ECO:0000269|PubMed:12403812, ECO:0000269|PubMed:15659651, ECO:0000269|PubMed:16943179, ECO:0000269|PubMed:20551181, ECO:0000269|PubMed:24121310}.;
- Disease
- DISEASE: Note=A chromosomal aberration involving PCM1 is found in papillary thyroid carcinomas (PTCs) (PubMed:10980597). Translocation t(8;10)(p21.3;q11.2) with RET links the protein kinase domain of RET to the major portion of PCM1 (PubMed:10980597). {ECO:0000269|PubMed:10980597}.; DISEASE: Note=A chromosomal aberration involving PCM1 is found in a variety of hematological malignancies including atypical chronic myeloid leukemia (atypical CML) and T-cell lymphoma (PubMed:15805263, PubMed:16034466, PubMed:16091753, PubMed:16769584, PubMed:16424865). Translocation t(8;9)(p22;p24) with JAK2 links the protein kinase domain of JAK2 to the major portion of PCM1 (PubMed:15805263, PubMed:16034466, PubMed:16091753, PubMed:16769584, PubMed:16424865). {ECO:0000269|PubMed:15805263, ECO:0000269|PubMed:16034466, ECO:0000269|PubMed:16091753, ECO:0000269|PubMed:16424865, ECO:0000269|PubMed:16769584}.;
- Pathway
- Prader-Willi and Angelman Syndrome;Regulation of PLK1 Activity at G2/M Transition;Recruitment of mitotic centrosome proteins and complexes;Loss of Nlp from mitotic centrosomes;Loss of proteins required for interphase microtubule organization from the centrosome;Centrosome maturation;AURKA Activation by TPX2;G2/M Transition;Mitotic G2-G2/M phases;Recruitment of NuMA to mitotic centrosomes;Mitotic Prometaphase;M Phase;Cell Cycle;Cell Cycle, Mitotic;Anchoring of the basal body to the plasma membrane;Cilium Assembly;Organelle biogenesis and maintenance
(Consensus)
Recessive Scores
- pRec
- 0.135
Intolerance Scores
- loftool
- 0.819
- rvis_EVS
- -0.32
- rvis_percentile_EVS
- 30.93
Haploinsufficiency Scores
- pHI
- 0.525
- hipred
- hipred_score
- ghis
- 0.571
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.987
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pcm1
- Phenotype
- behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- pcm1
- Affected structure
- whole organism
- Phenotype tag
- abnormal
- Phenotype quality
- curved lateral
Gene ontology
- Biological process
- G2/M transition of mitotic cell cycle;neuron migration;centrosome cycle;regulation of G2/M transition of mitotic cell cycle;interkinetic nuclear migration;cytoplasmic microtubule organization;microtubule anchoring;microtubule anchoring at centrosome;social behavior;intraciliary transport involved in cilium assembly;negative regulation of neurogenesis;cilium assembly;protein localization to centrosome;positive regulation of intracellular protein transport;neuronal stem cell population maintenance;ciliary basal body-plasma membrane docking;non-motile cilium assembly
- Cellular component
- pericentriolar material;cytoplasm;centrosome;centriole;cytosol;membrane;nuclear membrane;protein-containing complex;centriolar satellite;ciliary transition zone;ciliary basal body;apical part of cell;non-motile cilium
- Molecular function
- protein binding;identical protein binding