PCM1

pericentriolar material 1

Basic information

Region (hg38): 8:17922841-18029948

Links

ENSG00000078674 ∙ NCBI:5108 ∙ OMIM:600299 ∙ HGNC:8727 ∙ Uniprot:Q15154 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PCM1 gene.

• Inborn genetic diseases (125 variants)
• not provided (27 variants)
• Thyroid cancer, nonmedullary, 1 (1 variants)
• not specified (1 variants)
• PCM1-related condition (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.

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				9	5	14
missense			123	10	2	135
nonsense			2	1		3
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding						0
Total	0	0	125	20	7

Variants in PCM1

This is a list of pathogenic ClinVar variants found in the PCM1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
8-17935666-A-G		not specified	Uncertain significance (Aug 30, 2021)
8-17935694-G-T		not specified	Uncertain significance (Nov 22, 2022)
8-17937149-C-A		not specified	Uncertain significance (Mar 20, 2023)
8-17937159-C-T		not specified	Uncertain significance (Sep 20, 2023)
8-17937339-A-G		not specified	Uncertain significance (Aug 21, 2023)
8-17937344-C-G		not specified	Uncertain significance (Jan 08, 2024)
8-17937350-C-G		not specified	Uncertain significance (Feb 15, 2023)
8-17937353-C-T		not specified	Uncertain significance (Dec 14, 2021)
8-17937354-G-A		not specified	Uncertain significance (Mar 06, 2023)
8-17937364-C-G		not specified	Uncertain significance (Nov 15, 2021)
8-17938744-G-C		not specified	Uncertain significance (Jan 20, 2023)
8-17938792-G-T		not specified	Uncertain significance (Jul 05, 2023)
8-17938827-T-A		not specified	Uncertain significance (Dec 19, 2023)
8-17938861-A-G		not specified	Uncertain significance (Dec 21, 2022)
8-17938891-C-T		not specified	Likely benign (Dec 01, 2023)
8-17938897-G-A		not specified	Uncertain significance (Jul 12, 2023)
8-17938903-C-T		not specified	Uncertain significance (Jun 29, 2023)
8-17938904-A-C			Likely benign (Nov 01, 2022)
8-17939790-C-T		not specified	Uncertain significance (Dec 28, 2022)
8-17939859-C-T		not specified	Uncertain significance (Jan 24, 2023)
8-17947198-C-G		not specified	Uncertain significance (Aug 30, 2021)
8-17947353-G-A		not specified	Uncertain significance (May 18, 2022)
8-17950651-G-A		not specified	Uncertain significance (Dec 21, 2023)
8-17950696-G-A		not specified	Uncertain significance (Oct 26, 2022)
8-17950713-C-T		not specified	Uncertain significance (Feb 06, 2023)

GnomAD

Source: gnomAD

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: dbNSFP

• 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
• 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