CENPM

centromere protein M, the group of Constitutive centromere associated network|Minor histocompatibility antigens

Basic information

Region (hg38): 22:41927514-41947152

Previous symbols: [ "C22orf18" ]

Links

ENSG00000100162NCBI:79019OMIM:610152HGNC:18352Uniprot:Q9NSP4AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CENPM 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
0
missense
6
clinvar
6
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 6 0 0

Variants in CENPM

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

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

Position Type Phenotype Significance ClinVar
22-41939124-C-T not specified Uncertain significance (Dec 06, 2023)3142398
22-41939154-C-G not specified Uncertain significance (Feb 07, 2023)2466823
22-41943620-C-T not specified Uncertain significance (May 28, 2023)2552433
22-41943672-G-A not specified Uncertain significance (Feb 05, 2024)3142397
22-41943696-G-A not specified Uncertain significance (May 03, 2023)2552581
22-41946436-A-G not specified Uncertain significance (Jun 02, 2024)3265934
22-41947061-G-A not specified Uncertain significance (Feb 26, 2024)3142396

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CENPMprotein_codingprotein_codingENST00000215980 68444
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.01500.8861257020151257170.0000597
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.543911070.8520.000006141145
Missense in Polyphen2638.1220.68202415
Synonymous-0.3335148.11.060.00000262384
Loss of Function1.3848.280.4834.02e-796

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00008750.0000875
Ashkenazi Jewish0.0004030.000397
East Asian0.0001090.000109
Finnish0.000.00
European (Non-Finnish)0.00004420.0000440
Middle Eastern0.0001090.000109
South Asian0.000.00
Other0.0001640.000163

dbNSFP

Source: dbNSFP

Function
FUNCTION: Component of the CENPA-NAC (nucleosome-associated) complex, a complex that plays a central role in assembly of kinetochore proteins, mitotic progression and chromosome segregation. The CENPA-NAC complex recruits the CENPA-CAD (nucleosome distal) complex and may be involved in incorporation of newly synthesized CENPA into centromeres. {ECO:0000269|PubMed:16716197}.;
Pathway
Signal Transduction;Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal;Amplification of signal from the kinetochores;Mitotic Spindle Checkpoint;Cell Cycle Checkpoints;RHO GTPases Activate Formins;Nucleosome assembly;RHO GTPase Effectors;Signaling by Rho GTPases;Chromosome Maintenance;Deposition of new CENPA-containing nucleosomes at the centromere;Mitotic Prometaphase;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;M Phase;Cell Cycle;Resolution of Sister Chromatid Cohesion;Cell Cycle, Mitotic (Consensus)

Recessive Scores

pRec
0.115

Intolerance Scores

loftool
0.419
rvis_EVS
-0.1
rvis_percentile_EVS
46.49

Haploinsufficiency Scores

pHI
0.562
hipred
N
hipred_score
0.474
ghis
0.704

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
E
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.923

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Cenpm
Phenotype

Gene ontology

Biological process
CENP-A containing nucleosome assembly
Cellular component
condensed chromosome kinetochore;nucleoplasm;cytosol
Molecular function