CENPF

centromere protein F

Basic information

Region (hg38): 1:214603185-214664574

Links

ENSG00000117724NCBI:1063OMIM:600236HGNC:1857Uniprot:P49454AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • Stromme syndrome (Strong), mode of inheritance: AR
  • Stromme syndrome (Strong), mode of inheritance: AR
  • Stromme syndrome (Strong), mode of inheritance: AR
  • Stromme syndrome (Supportive), mode of inheritance: AR
  • Stromme syndrome (Supportive), mode of inheritance: AR
  • Stromme syndrome (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Stromme syndromeARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingCraniofacial; Gastrointestinal; Neurologic; Renal25564561; 26820108

ClinVar

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

  • Inborn_genetic_diseases (376 variants)
  • not_provided (339 variants)
  • Stromme_syndrome (67 variants)
  • CENPF-related_disorder (67 variants)
  • not_specified (47 variants)
  • Neurodevelopmental_delay (2 variants)
  • Microcephaly (2 variants)
  • Susceptibility_to_severe_COVID-19 (1 variants)
  • Cystinuria (1 variants)
  • Primary_ciliary_dyskinesia_29 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CENPF gene is commonly pathogenic or not. These statistics are base on transcript: NM_000016343.4. 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.

EffectPLPVUSLBBSum
synonymous
3
clinvar
102
clinvar
6
clinvar
111
missense
1
clinvar
459
clinvar
61
clinvar
9
clinvar
530
nonsense
12
clinvar
13
clinvar
2
clinvar
27
start loss
0
frameshift
8
clinvar
15
clinvar
2
clinvar
25
splice donor/acceptor (+/-2bp)
3
clinvar
7
clinvar
3
clinvar
13
Total 23 36 469 163 15

Highest pathogenic variant AF is 0.00031911235

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CENPFprotein_codingprotein_codingENST00000366955 1961394
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.88e-361.0012538803601257480.00143
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.029714731.47e+31.000.000072820620
Missense in Polyphen375400.250.936916078
Synonymous-0.2975775681.020.00002975506
Loss of Function4.14791300.6080.000006371848

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001910.00190
Ashkenazi Jewish0.001890.00189
East Asian0.0007480.000707
Finnish0.0004200.000416
European (Non-Finnish)0.001920.00187
Middle Eastern0.0007480.000707
South Asian0.001620.00157
Other0.001720.00163

dbNSFP

Source: dbNSFP

Function
FUNCTION: Required for kinetochore function and chromosome segregation in mitosis. Required for kinetochore localization of dynein, LIS1, NDE1 and NDEL1. Regulates recycling of the plasma membrane by acting as a link between recycling vesicles and the microtubule network though its association with STX4 and SNAP25. Acts as a potential inhibitor of pocket protein-mediated cellular processes during development by regulating the activity of RB proteins during cell division and proliferation. May play a regulatory or permissive role in the normal embryonic cardiomyocyte cell cycle and in promoting continued mitosis in transformed, abnormally dividing neonatal cardiomyocytes. Interaction with RB directs embryonic stem cells toward a cardiac lineage. Involved in the regulation of DNA synthesis and hence cell cycle progression, via its C-terminus. Has a potential role regulating skeletal myogenesis and in cell differentiation in embryogenesis. Involved in dendritic cell regulation of T-cell immunity against chlamydia. {ECO:0000269|PubMed:12974617, ECO:0000269|PubMed:17600710, ECO:0000269|PubMed:7542657, ECO:0000269|PubMed:7651420}.;
Disease
DISEASE: Stromme syndrome (STROMS) [MIM:243605]: An autosomal recessive congenital disorder characterized by intestinal atresia, ocular anomalies, microcephaly, and renal and cardiac abnormalities in some patients. The disease has features of a ciliopathy, and lethality in early childhood is observed in severe cases. {ECO:0000269|PubMed:25564561, ECO:0000269|PubMed:26820108}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway
Mitotic G2-G2-M phases;Gastric Cancer Network 1;Signal Transduction;Polo-like kinase mediated events;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;RHO GTPase Effectors;Signaling by Rho GTPases;G2/M Transition;Mitotic G2-G2/M phases;Mitotic Prometaphase;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;M Phase;Cell Cycle;Resolution of Sister Chromatid Cohesion;Cell Cycle, Mitotic;FOXM1 transcription factor network (Consensus)

Recessive Scores

pRec
0.148

Intolerance Scores

loftool
0.968
rvis_EVS
4.96
rvis_percentile_EVS
99.81

Haploinsufficiency Scores

pHI
0.821
hipred
Y
hipred_score
0.647
ghis
0.543

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
E
essential_gene_gene_trap
H
gene_indispensability_pred
E
gene_indispensability_score
0.730

Gene Damage Prediction

AllRecessiveDominant
MendelianHighHighHigh
Primary ImmunodeficiencyHighHighHigh
CancerHighHighHigh

Mouse Genome Informatics

Gene name
Cenpf
Phenotype
muscle phenotype; cellular phenotype; growth/size/body region phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);

Zebrafish Information Network

Gene name
cenpf
Affected structure
trunk
Phenotype tag
abnormal
Phenotype quality
curved

Gene ontology

Biological process
mitotic cell cycle;kidney development;chromosome segregation;mitotic spindle assembly checkpoint;muscle organ development;cell population proliferation;regulation of G2/M transition of mitotic cell cycle;protein transport;regulation of striated muscle tissue development;ventricular system development;cell differentiation;response to drug;negative regulation of transcription, DNA-templated;cell division;metaphase plate congression;kinetochore assembly;regulation of cell cycle;DNA biosynthetic process
Cellular component
chromosome, centromeric region;kinetochore;chromatin;spindle pole;condensed chromosome outer kinetochore;nucleus;nuclear envelope;nucleoplasm;cytoplasm;centrosome;spindle;cytosol;axoneme;nuclear matrix;midbody;ciliary basal body;pronucleus;perinuclear region of cytoplasm;ciliary transition fiber
Molecular function
chromatin binding;protein binding;protein C-terminus binding;transcription factor binding;protein homodimerization activity;dynein complex binding