CENPF
Basic information
Region (hg38): 1:214603185-214664574
Links
Phenotypes
GenCC
Source:
- 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:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Stromme syndrome | AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Craniofacial; Gastrointestinal; Neurologic; Renal | 25564561; 26820108 |
ClinVar
This is a list of variants' phenotypes submitted to
- 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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 102 | 111 | ||||
missense | 459 | 61 | 530 | |||
nonsense | 12 | 13 | 27 | |||
start loss | 0 | |||||
frameshift | 15 | 25 | ||||
splice donor/acceptor (+/-2bp) | 13 | |||||
Total | 23 | 36 | 469 | 163 | 15 |
Highest pathogenic variant AF is 0.00031911235
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
CENPF | protein_coding | protein_coding | ENST00000366955 | 19 | 61394 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.88e-36 | 1.00 | 125388 | 0 | 360 | 125748 | 0.00143 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.0297 | 1473 | 1.47e+3 | 1.00 | 0.0000728 | 20620 |
Missense in Polyphen | 375 | 400.25 | 0.93691 | 6078 | ||
Synonymous | -0.297 | 577 | 568 | 1.02 | 0.0000297 | 5506 |
Loss of Function | 4.14 | 79 | 130 | 0.608 | 0.00000637 | 1848 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00191 | 0.00190 |
Ashkenazi Jewish | 0.00189 | 0.00189 |
East Asian | 0.000748 | 0.000707 |
Finnish | 0.000420 | 0.000416 |
European (Non-Finnish) | 0.00192 | 0.00187 |
Middle Eastern | 0.000748 | 0.000707 |
South Asian | 0.00162 | 0.00157 |
Other | 0.00172 | 0.00163 |
dbNSFP
Source:
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | High | High | High |
Primary Immunodeficiency | High | High | High |
Cancer | High | High | High |
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