CENPM

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

Basic information

Region (hg38): 22:41938736-41947152

Previous symbols: [ "C22orf18" ]

Links

ENSG00000100162 ∙ NCBI:79019 ∙ OMIM:610152 ∙ HGNC:18352 ∙ Uniprot:Q9NSP4 ∙ 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 CENPM gene.

• Inborn genetic diseases (3 variants)

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			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	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)
22-41939154-C-G		not specified	Uncertain significance (Feb 07, 2023)
22-41943620-C-T		not specified	Uncertain significance (May 28, 2023)
22-41943672-G-A		not specified	Uncertain significance (Feb 05, 2024)
22-41943696-G-A		not specified	Uncertain significance (May 03, 2023)
22-41947061-G-A		not specified	Uncertain significance (Feb 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CENPM	protein_coding	protein_coding	ENST00000215980	6	8444

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0150	0.886	125702	0	15	125717	0.0000597

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.543	91	107	0.852	0.00000614	1145
Missense in Polyphen		26	38.122	0.68202		415
Synonymous	-0.333	51	48.1	1.06	0.00000262	384
Loss of Function	1.38	4	8.28	0.483	4.02e-7	96

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000875	0.0000875
Ashkenazi Jewish	0.000403	0.000397
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000442	0.0000440
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.000164	0.000163

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Cenpm

Gene ontology

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