CENPS

centromere protein S, the group of Constitutive centromere associated network

Basic information

Region (hg38): 1:10430433-10442808

Previous symbols: [ "APITD1", "MHF1" ]

Links

ENSG00000175279NCBI:378708OMIM:609130HGNC:23163Uniprot:Q8N2Z9AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CENPS 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
4
clinvar
4
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 4 0 0

Variants in CENPS

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

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

Position Type Phenotype Significance ClinVar
1-10430528-A-C not specified Uncertain significance (Jun 26, 2023)2606347
1-10430542-G-A not specified Uncertain significance (Feb 10, 2022)3142427
1-10430550-G-T not specified Uncertain significance (Jun 30, 2024)3490415
1-10433906-A-G not specified Uncertain significance (Feb 03, 2022)3142423
1-10433933-C-T not specified Uncertain significance (May 01, 2024)3265944
1-10434664-T-G not specified Uncertain significance (May 07, 2024)3265948
1-10440352-C-T not specified Uncertain significance (Apr 08, 2024)3265945
1-10440380-T-A not specified Uncertain significance (Feb 26, 2024)3142424

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CENPSprotein_codingprotein_codingENST00000602787 522052
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.000005750.2691256900581257480.000231
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-1.1111686.91.330.000004181078
Missense in Polyphen2422.341.0743294
Synonymous0.5103033.80.8880.00000188291
Loss of Function0.024588.070.9914.28e-791

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0006140.000614
Ashkenazi Jewish0.0003970.000397
East Asian0.00005440.0000544
Finnish0.000.00
European (Non-Finnish)0.0002390.000237
Middle Eastern0.00005440.0000544
South Asian0.0001320.000131
Other0.0004970.000489

dbNSFP

Source: dbNSFP

Function
FUNCTION: DNA-binding component of the Fanconi anemia (FA) core complex. Required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage (PubMed:20347428, PubMed:20347429). In complex with CENPX (MHF heterodimer), crucial cofactor for FANCM in both binding and ATP-dependent remodeling of DNA. Stabilizes FANCM (PubMed:20347428, PubMed:20347429). In complex with CENPX and FANCM (but not other FANC proteins), rapidly recruited to blocked forks and promotes gene conversion at blocked replication forks (PubMed:20347428). In complex with CENPT, CENPW and CENPX (CENP-T-W-S-X heterotetramer), involved in the formation of a functional kinetochore outer plate, which is essential for kinetochore-microtubule attachment and faithful mitotic progression (PubMed:19620631). As a component of MHF and CENP-T-W-S-X complexes, binds DNA and bends it to form a nucleosome-like structure (PubMed:20347428, PubMed:22304917). DNA- binding function is fulfilled in the presence of CENPX, with the following preference for DNA substates: Holliday junction > double-stranded > splay arm > single-stranded. Does not bind DNA on its own (PubMed:20347428, PubMed:20347429). {ECO:0000269|PubMed:19620631, ECO:0000269|PubMed:20347428, ECO:0000269|PubMed:20347429, ECO:0000269|PubMed:22304917}.;
Pathway
Fanconi anemia pathway - Homo sapiens (human);Fanconi Anemia Pathway;DNA Repair;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;Fanconi anemia pathway;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
0.266

Intolerance Scores

loftool
rvis_EVS
0.21
rvis_percentile_EVS
67.72

Haploinsufficiency Scores

pHI
hipred
N
hipred_score
0.146
ghis
0.573

Essentials

essential_gene_CRISPR
essential_gene_CRISPR2
essential_gene_gene_trap
N
gene_indispensability_pred
gene_indispensability_score

Mouse Genome Informatics

Gene name
Cenps
Phenotype

Gene ontology

Biological process
resolution of meiotic recombination intermediates;DNA repair;cellular response to DNA damage stimulus;replication fork processing;positive regulation of protein ubiquitination;CENP-A containing nucleosome assembly;interstrand cross-link repair;cell division;kinetochore assembly
Cellular component
condensed chromosome kinetochore;nucleoplasm;cytosol;Fanconi anaemia nuclear complex;FANCM-MHF complex
Molecular function
DNA binding;chromatin binding;double-stranded DNA binding;protein binding;protein heterodimerization activity