HGNC Approved Gene Symbol: TBCK
SNOMEDCT: 1172628002;
Cytogenetic location: 4q24 Genomic coordinates (GRCh38): 4:106,041,599-106,316,683 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 4q24 | Hypotonia, infantile, with psychomotor retardation and characteristic facies 3 | 616900 | Autosomal recessive | 3 |
TBCK is a conserved protein kinase that associates with the mitotic apparatus and regulates cell size, cell proliferation, and MTOR (601231) signaling (Liu et al., 2013; Wu et al., 2014).
By sequence analysis and RT-PCR of HEK293 cell total RNA, Liu et al. (2013) cloned human TBCK. The deduced 893-amino acid protein has a predicted molecular mass of 99 kD. It contains an N-terminal kinase domain, a central TBC domain (see 609850), and a C-terminal rhodanese (TST; 180370) homology (RHOD) domain. TBCK is highly conserved in worms, flies, and vertebrates. Immunoblot analysis showed variable expression of TBCK in all human and other mammalian cell lines examined. Immunofluorescence showed that TBCK colocalized with gamma-tubulin (TUBG1; 191135) in addition to punctate distribution in HEK293 cells. However, in HeLa cells, TBCK failed to colocalize with gamma-tubulin and instead localized near the nucleus and centrosomes.
Wu et al. (2014) identified TBCK in a HeLa cDNA expression library screen using pooled autoantibodies from patients with systemic lupus erythematosus (SLE; 152700). Sequence analysis and RT-PCR of human cell lines revealed 9 TBCK splice variants of 2 major types. Six variants were long type and encoded isoforms possessing TBC, RHOD, and STYKc kinase domains, and 3 variants were short type and encoded isoforms lacking the STYKc kinase domain. Western blot analysis showed that TBCK had an apparent molecular mass of 95 kD and was robustly expressed in whole cell lysates and cytosolic fractions of several human cell lines, with weaker expression in nuclear fractions. An additional band of lower molecular mass was observed in HepG2 and HEK293FT cells. In HeLa cells, GFP-tagged TBCK localized mainly to cytoplasm during interphase and colocalized with spindle fibers of the mitotic apparatus during metaphase. RNA sequencing analysis showed that several long TBCK variants were downregulated in tumor tissue compared with normal tissue.
Using fluorescence microscopy, cell count, and MTT assays, Liu et al. (2013) showed that small interfering RNA (siRNA)-mediated TBCK silencing decreased cell size and inhibited cell proliferation in HEK293 cells. Immunofluorescence analysis revealed that siRNA-mediated TBCK depletion led to a decrease in F-actin and disrupted stress fibers, without affecting cortical actin or microtubule structures. Western blot and immunofluorescence analyses showed that TBCK knockdown decreased phosphorylation and protein levels of MTOR and also decreased protein levels of the MTOR complex (MTORC) components Raptor (RPTOR; 607130), Rictor (609022), and MLST8 (612190). TBCK knockdown also inhibited phosphorylation of downstream components of the MTOR pathway, including 4EBP1 (EIF4EBP1; 602223), p70S6K (see 601684), and AKT (AKT1; 164730), and decreased protein levels of 4EBP1, but not p70S6K or AKT. Quantitative RT-PCR analysis showed that TBCK knockdown repressed expression of MTOR, Raptor, Rictor, MLST8, and 4EBP1, but not p70S6K or AKT, at the mRNA level. TBCK depletion had no effect on MAPK or PDK1 (PDPK1; 605213)/AKT pathways. Liu et al. (2013) concluded that TBCK plays roles in cell proliferation, cell growth, and actin organization, possibly by modulating the MTOR pathway.
Wu et al. (2014) found that overexpression of a long TBCK isoform decreased cellular proliferation rates in HeLa cells. Flow cytometry revealed that TBCK-overexpressing HeLa cells accumulated at S phase of the cell cycle but retained normal DNA synthesis, suggesting that long TBCK isoforms may suppress cellular proliferation during S phase. RNA interference-mediated knockdown of TBCK increased proliferation rates of normal and TBCK-overexpressing HeLa cells.
Wu et al. (2014) reported that the TBCK gene contains at least 26 exons and is subject to extensive alternative splicing.
Gross (2016) mapped the TBCK gene to chromosome 4q24 based on an alignment of the TBCK sequence (GenBank BC009208) with the genomic sequence (GRCh38).
In 2 sibs, born of consanguineous Saudi parents (family 10DG1670), with infantile hypotonia with psychomotor retardation and characteristic facies-3 (IHPRF3; 616900), Alazami et al. (2015) identified a homozygous splice site mutation in the TBCK gene (616899.0001). The patients were part of a large cohort of 143 multiplex consanguineous families with various neurodevelopmental disorders who underwent whole-exome sequencing.
In 5 patients, including 2 sisters, with IHPRF3, Chong et al. (2016) identified homozygous mutations in the TBCK gene (616899.0002-616899.0004). The mutations were found by whole-exome sequencing. Two unrelated patients of Puerto Rican descent carried the same truncating mutation (R126X; 616899.0002). Cells from 1 of these patients showed near absence of the full-length TBCK 101-kD isoform and decreased levels of the 71-kD shorter isoform, consistent with a loss of function.
In 13 patients from 9 unrelated families with IHPRF3, Bhoj et al. (2016) identified homozygous or compound heterozygous mutations in the TBCK gene (see, e.g., 616899.0001-616899.0002; 616899.0005-616899.0008). The mutations, which were found by whole-exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the families. Studies of patient cells with a splice site mutation (616899.0001) showed undetectable levels of the TBCK protein. Studies of patient cells with a different frameshift mutation (616899.0005) showed significantly decreased phosphorylation of phosphoribosomal protein S6 (RPS6; 180460) compared to controls, suggesting downregulation of the mTOR signaling pathway. The addition of leucine to the culture media induced an upregulation of basal mTOR signaling as evidenced by increased levels of phosphorylated RPS6; these findings suggested a possible avenue for directed therapies for this disorder. Four patients from 3 families of Hispanic descent carried the R126X mutation, suggesting a founder effect in this population.
In 2 sibs, born of consanguineous Saudi parents (family 10DG1670), with infantile hypotonia with psychomotor retardation and characteristic facies-3 (IHPRF3; 616900), Alazami et al. (2015) identified a homozygous c.1708+1G-A (c.1708+1G-A, NM_033115) transition in the TBCK gene, predicted to result in a splicing defect. The mutation was found by whole-exome sequencing and segregated with the disorder in the family. Functional studies and studies of patient cells were not performed. The patients had severe global developmental delay, epilepsy, dysmorphic features, hypotonia, and diffuse brain atrophy. The patients were part of a large cohort of 143 multiplex consanguineous families with various neurodevelopmental disorders who underwent whole-exome sequencing. Bhoj et al. (2016) provided follow-up of the sibs reported by Alazami et al. (2015), and stated that the mutation was a homozygous c.1897+1G-A transition (c.1897+1G-A, NM_001163435.2) predicted to result in a frameshift. One of the patients died at age 5 years. Patient cells showed no detectable TBCK protein, consistent with a loss of function. The variant was found at a low frequency (0.000008319) in the ExAC database.
In 2 unrelated patients of Puerto Rican descent with infantile hypotonia with psychomotor retardation and characteristic facies-3 (IHPRF3; 616900), Chong et al. (2016) identified a homozygous c.376C-T transition (c.376C-T, NM_001163435.2) in the TBCK gene, resulting in an arg126-to-ter (R126X) substitution. The mutation was found by whole-exome sequencing and was present at a low frequency (0.5208%) in the ExAC Latino database (v.0.3). Cells from 1 patient showed near absence of the full-length TBCK 101-kD isoform and decreased levels of the 71-kD shorter isoform.
Bhoj et al. (2016) identified a homozygous R126X mutation in 2 unrelated patients of Hispanic descent with IHPRF3. Two affected sibs from another family of Hispanic descent were compound heterozygous for R126X and a deletion of exons 7 to 22 of the TBCK gene. The R126X mutation occurred in the protein kinase domain. The mutations, which were found by whole-exome sequencing and confirmed by Sanger sequencing, were filtered through the dbSNP, 1000 Genomes Project, and Exome Variant Server databases, and segregated with the disorder in the families. The R126X variant was found at a low frequency (0.0001426) in the ExAC database.
In 2 sisters, born of consanguineous Lebanese parents, with infantile hypotonia with psychomotor retardation and characteristic facies-3 (IHPRF3; 616900), Chong et al. (2016) identified a homozygous c.1363A-T transversion in the TBCK gene, resulting in a lys455-to-ter (K455X) substitution. The mutation, which was found by a combination of whole-exome sequencing and linkage analysis, segregated with the disorder in the family. The variant was present at a very low frequency (0.0107%) in the ExAC Latino database (v.0.3). Functional studies and studies on patient cells were not performed.
In a 2-year-old boy, born of consanguineous Egyptian parents, with infantile hypotonia with psychomotor retardation and characteristic facies-3 (IHPRF3; 616900), Chong et al. (2016) identified a homozygous c.1532G-A transition (c.1532G-A, NM_001163435.2) in the TBCK gene, resulting in an arg511-to-his (R511H) substitution at a highly conserved residue in the TBC1 domain. The mutation, which was found by whole-exome sequencing, was not present in the 1000 Genomes Project, Exome Sequencing Project, or ExAC control databases. Molecular modeling studies predicted that the mutation would impair GAP activity, but direct functional studies and studies on patient cells were not performed.
In a 5-year-old boy, born of unrelated Syrian parents, with infantile hypotonia with psychomotor retardation and characteristic facies-3 (IHPRF3; 616900), Bhoj et al. (2016) identified a homozygous 2-bp insertion (c.831_832insTA, NM_001163435.2) in the TBCK gene, resulting in a frameshift and premature termination (Pro278TyrfsTer18). The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, was filtered through the dbSNP, 1000 Genomes Project, and Exome Variant Server databases, and segregated with the disorder in the family. Patient cells showed significantly decreased phosphorylation of phosphoribosomal protein S6 (RPS6; 180460) compared to controls, suggesting downregulation of the mTOR signaling pathway. The addition of leucine to the culture media induced an upregulation of basal mTOR signaling as evidenced by increased levels of phosphorylated RPS6.
In 2 sisters of mixed European descent with infantile hypotonia with psychomotor retardation and characteristic facies-3 (IHPRF3; 616900), Bhoj et al. (2016) identified compound heterozygous mutations in the TBCK gene: a c.2060-2A-G transition (c.2060-2A-G, NM_001163435.2), resulting in a splice site defect and a frameshift, and a 4-bp deletion (c.803_806delTGAA; 616899.0007), resulting in a frameshift and premature termination (Met268ArgfsTer26). The mutations, which were found by whole-exome sequencing and confirmed by Sanger sequencing, were filtered through the dbSNP, 1000 Genomes Project, and Exome Variant Server databases, and segregated with the disorder in the family. Functional studies and studies of patient cells were not performed.
For discussion of the 4-bp deletion (c.803_806delTGAA, NM_001163435.2), resulting in a frameshift and premature termination (Met268ArgfsTer26), in the TBCK gene that was found in compound heterozygous state in 2 sisters with infantile hypotonia with psychomotor retardation and characteristic facies-3 (IHPRF3; 616900) by Bhoj et al. (2016), see 616899.0006.
In 2 sibs, born of consanguineous Algerian parents, with infantile hypotonia with psychomotor retardation and characteristic facies-3 (IHPRF3; 616900), Bhoj et al. (2016) identified a homozygous 1-bp deletion (c.1370delA, NM_001163435.2) in the TBCK gene, resulting in a frameshift and premature termination (Asn457ThrfsTer15). The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, was filtered through the dbSNP, 1000 Genomes Project, and Exome Variant Server databases, and segregated with the disorder in the family. Functional studies and studies of patient cells were not performed.
Alazami, A. M., Patel, N., Shamseldin, H. E., Anazi, S., Al-Dosari, M. S., Alzahrani, F., Hijazi, H., Alshammari, M., Aldahmesh, M. A., Salih, M. A., Faqeih, E., Alhashem, A., and 41 others. Accelerating novel candidate gene discovery in neurogenetic disorders via whole-exome sequencing of prescreened multiplex consanguineous families. Cell Rep. 10: 148-161, 2015. [PubMed: 25558065] [Full Text: https://doi.org/10.1016/j.celrep.2014.12.015]
Bhoj, E. J., Li, D., Harr, M., Edvardson, S., Elpeleg, O., Chisholm, E., Juusola, J., Douglas, G., Guillen Sacoto, M. J., Siquier-Pernet, K., Saadi, A., Bole-Feysot, C., and 12 others. Mutations in TBCK, encoding TBC1-domain-containing kinase, lead to a recognizable syndrome of intellectual disability and hypotonia. Am. J. Hum. Genet. 98: 782-788, 2016. [PubMed: 27040691] [Full Text: https://doi.org/10.1016/j.ajhg.2016.03.016]
Chong, J. X., Caputo, V., Phelps, I. G., Stella, L., Worgan, L., Dempsey, J. C., Nguyen, A., Leuzzi, V., Webster, R., Pizzuti, A., Marvin, C. T., Ishak, G. E., Ardern-Holmes, S., Richmond, Z., Univerisity of Washington Center for Mendelian Genomics, Bamshad, M. J., Ortiz-Gonzalez, X. R., Tartaglia, M., Chopra, M., Doherty, D. Recessive inactivating mutations in TBCK, encoding a Rab GTPase-activating protein, cause severe infantile syndromic encephalopathy. Am. J. Hum. Genet. 98: 772-781, 2016. [PubMed: 27040692] [Full Text: https://doi.org/10.1016/j.ajhg.2016.01.016]
Gross, M. B. Personal Communication. Baltimore, Md. 4/8/2016.
Liu, Y., Yan, X., Zhou, T. TBCK influences cell proliferation, cell size and mTOR signaling pathway. PLoS One 8: e71349, 2013. Note: Electronic Article. [PubMed: 23977024] [Full Text: https://doi.org/10.1371/journal.pone.0071349]
Wu, J., Li, Q., Li, Y., Lin, J., Yang, D., Zhu, G., Wang, L., He, D., Lu, G., Zeng, C. A long type of TBCK is a novel cytoplasmic and mitotic apparatus-associated protein likely suppressing cell proliferation. (Letter) J. Genet. Genomics 41: 69-72, 2014. [PubMed: 24576458] [Full Text: https://doi.org/10.1016/j.jgg.2013.12.006]