Alternative titles; symbols
HGNC Approved Gene Symbol: FOCAD
Cytogenetic location: 9p21.3 Genomic coordinates (GRCh38): 9:20,655,625-20,995,950 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 9p21.3 | Liver disease, severe congenital | 619991 | Autosomal recessive | 3 |
By sequencing clones obtained from a size-fractionated fetal brain cDNA library, Nagase et al. (2001) cloned FOCAD, which they designated KIAA1797. The deduced protein contains 1,281 amino acids. RT-PCR analysis revealed low to moderate FOCAD expression in all adult and fetal tissues examined except spleen, which showed little to no expression. Expression was highest in adult brain, liver, kidney, ovary, and spinal cord and in fetal brain and liver. Low to moderate expression was detected in all specific adult brain regions examined, with highest levels in amygdala, cerebellum, caudate nucleus, and hippocampus.
Using real-time RT-PCR, Brockschmidt et al. (2012) detected variable KIAA1797 expression in all adult and fetal tissues examined. In adult tissues, expression was highest in brain, followed by testis, muscle, pancreas, heart, ovary, small intestine, placenta, prostate, thymus, kidney, colon, liver, lung, spleen, and leukocytes. In fetal tissues, expression was highest in brain, followed by muscle, kidney, heart, thymus, lung, liver, and spleen. Kiaa1797 was expressed in granule cell layer and hilus of mouse dentate gyrus. Immunofluorescence analysis of human astrocytes revealed colocalization of KIAA1797 with vinculin (VCL; 193065) at focal adhesions at the ends of actin stress fibers. Western blot analysis revealed KIAA1797 protein at an apparent molecular mass of about 200 kD in human white matter, cortex, and astrocytes.
Weren et al. (2015) found expression of the FOCAD gene in colonic epithelial cells.
Moreno Traspas et al. (2022) found cytosolic expression of FOCAD in HEK293T cells and human dermal fibroblasts. It did not localize to focal adhesions or centrosomes, and also was not enriched in endoplasmic reticulum (ER), Golgi, mitochondrial, or nuclear fractions.
Brockschmidt et al. (2012) determined that the FOCAD gene contains 46 exons and spans 337.6 kb.
Melton et al. (2010) stated that the FOCAD gene maps to chromosome 9p21.3.
Using real-time RT-PCR, Brockschmidt et al. (2012) found that expression of KIAA1797 was reduced in nearly all primary glioblastomas and in all glioblastoma primary cultures and cell lines examined. Reexpression of KIAA1797 in the LN18 and U87MG glioblastoma cell lines, which have homozygous KIAA1797 deletions, led to reduced colony formation and invasion capacity in vitro and reduced tumor lesions following implantation in nude mice. Immunoprecipitation analysis of transfected LN18 cells revealed direct interaction between KIAA1797 and vinculin.
Using FISH, Brockschmidt et al. (2012) found that the KIAA1797 gene was disrupted by a t(7;9) translocation and deletion in a human glioblastoma primary culture. The 5-prime UTR of KIAA1797 was translocated to the derivative chromosome 7, but the remainder of KIAA1797 was deleted and absent from the derivative chromosome 9. Array-based comparative genomic hybridization revealed that 6 of 13 primary glioblastomas had complete or partial deletions of KIAA1797, and microdeletions involving KIAA1797 were present in 5 of 10 glioblastoma primary cultures and glioblastoma cell lines. No glioblastomas or glioblastoma cell lines or primary cultures analyzed showed hypermethylation of the KIAA1797 gene.
Severe Congenital Liver Disease
In 14 patients from 10 unrelated families of various ethnic origins with severe congenital liver disease (SCOLIV; 619991), Moreno Traspas et al. (2022) identified biallelic mutations in the FOCAD gene (see, e.g., 614606.0001-614606.0006). The patients, who were all under 15 years of age, were ascertained through international collaborative efforts after genetic analysis identified the mutations. Six of the families were consanguineous. Most of the mutations were nonsense, frameshift, or splice site alterations, predicted to result in a loss of function, but there were also 3 missense variants at highly conserved residues. Western blot analysis of dermal fibroblasts derived from 2 patients showed nearly absent FOCAD expression in cellular extracts. There were also decreased levels of the SKIC2 protein (600478), suggesting that FOCAD may contribute to the stability of this RNA helicase. Similar results were obtained in FOCAD-null human hepatocytes in vitro, with the addition of decreased SKIC3 (614589). There was also increased secretion of the inflammatory marker CCL2 (158105). These findings and altered gene expression patterns suggested that loss of FOCAD disrupts hepatocyte homeostasis, which the authors postulated is the cell of origin responsible for the liver cirrhosis phenotype.
Associations Pending Confirmation
In 3 unrelated patients with colorectal cancer, Weren et al. (2015) identified 3 different germline heterozygous intragenic deletions affecting the FOCAD gene. The deletion breakpoints differed in each patient; each deletion spanned multiple exons and was predicted to result in a loss of function. The deletions in patients A and B included the miR-491 locus, which is located in intron 4 of the FOCAD gene. Tumor tissue available from patients B and C did not show somatic truncating mutations affecting FOCAD, suggesting haploinsufficiency as the underlying mechanism. Patient A was identified from a cohort of 41 patients who underwent microarray-based copy number variant (CNV) screening. Patients B and C were identified from a cohort of 1,232 patients with colorectal cancer. One of 12,400 controls had an intragenic FOCAD deletion. The deletions were thus enriched in the patient cohorts compared to controls (p = 0.0067). Patient A had multiple polyps and developed colorectal cancer at age 33 years. He had a family history of the disorder, but neither of his parents was affected and his 66-year-old mother also carried the deletion, suggesting incomplete penetrance. Of note, patient A also carried a de novo heterozygous pathogenic mutation in the POLE gene (L424V; 174762.0001) that is associated with susceptibility to colorectal cancer (CRC12; 615083) and may have contributed to the early onset in this patient. Patient B, who was diagnosed with colorectal cancer at age 62, and patient C, who had polyposis without colorectal cancer at age 64, both had a family history of colorectal cancer, but segregation studies of affected family members could not be performed. Functional studies of the variants were not performed. The authors hypothesized that additional germline variants may act as modifiers for disease penetrance, as observed in patient A.
MacFarland et al. (2022) reported a 6-year-old girl with juvenile polyposis associated with a germline heterozygous indel frameshift variant in the FOCAD gene (Leu454fs). The variant was inherited from her unaffected mother and was also present in the proband's maternal great-grandmother who reportedly had a history of polyposis. Another maternal relative reportedly had polyposis, but she was not sequenced. Functional studies of the variant and studies of patient cells were not performed, but it was predicted to result in a loss of function and haploinsufficiency.
Moreno Traspas et al. (2022) found that CRISPR/Cas9-mediated knockdown of the focad gene in zebrafish embryos resulted in decreased overall survival, growth retardation, and liver abnormalities, including swollen hepatocytes, steatosis, fibrosis, and hepatocyte apoptosis. Metabolic analysis showed dysregulation of multiple lipid species, and transcriptome analysis demonstrated differential expression of multiple genes involved in liver metabolism, inflammation, and RNA biology compared to wildtype.
In a boy, born of unrelated Indian parents (family 1), with severe congenital liver disease (SCOLIV; 619991), Moreno Traspas et al. (2022) identified compound heterozygous mutations in the FOCAD gene. One allele carried a c.2587C-T transition in exon 23, resulting in an arg863-to-ter (R863X) substitution, whereas the other allele was complex with 2 variants: a c.1687C-T transition in exon 16, resulting in an arg563-to-cys (R563C) substitution, and a c.3694G-C transversion in exon 33, resulting in an ala1232-to-pro (A1232P) substitution (614606.0002). The mutations, which were found by exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the family. R563C was present in the heterozygous state in gnomAD v.2.1.1 (2.0 x 10(-5)), whereas the other 2 mutations were absent in gnomAD. Western blot analysis of dermal fibroblasts derived from the patient showed nearly absent FOCAD expression in cellular extracts. There were also decreased levels of the SKIC2 protein (600478), suggesting that FOCAD may contribute to the stability of this RNA helicase.
For discussion of the complex mutation in the FOCAD gene consisting of a c.1687C-T transition and c.3694G-C transversion, resulting in an arg563-to-cys (R563C) and ala1232-to-pro (A1232P) substitution, respectively, that was found in compound heterozygous state in a patient with severe congenital liver disease (SCOLIV; 619991) by Moreno Traspas et al. (2022), see 614606.0001.
In a boy, born of unrelated French parents (family 2), with severe congenital liver disease (SCOLIV; 619991), Moreno Traspas et al. (2022) identified compound heterozygous mutations in the FOCAD gene: a c.5004G-C transversion, predicted to disrupt a splice donor site near exon 43, and a 1-bp duplication (c.2675dupC; 614606.0004) in exon 24, predicted to result in a frameshift and premature termination (Trp893LeufsTer32). The mutations, which were found by exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the family. Neither was present in the ExAC or gnomAD databases. Western blot analysis of dermal fibroblasts derived from the patient showed nearly absent FOCAD expression in cellular extracts. There were also decreased levels of the SKIC2 protein (600478), suggesting that FOCAD may contribute to the stability of this RNA helicase.
For discussion of the c.2675dupC mutation in exon 24 of the FOCAD gene, predicted to result in a frameshift and premature termination (Trp893LeufsTer32), that was found in compound heterozygous state in a patient with severe congenital liver disease (SCOLIV; 619991) by Moreno Traspas et al. (2022), see 614606.0003.
In 3 sibs, born of consanguineous Saudi parents (family 5), with severe congenital liver disease (SCOLIV; 619991), Moreno Traspas et al. (2022) identified a homozygous c.583C-T transition in exon 8 of the FOCAD gene, resulting in an arg195-to-ter (R195X) substitution in the N terminus. The mutation, which was found by exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the family. It was found at a low frequency in the heterozygous state in the ExAC (2.5 x 10(-5)) and gnomAD v.2.1.1 databases (1.4 x 10(-5)). Functional studies of the variant and studies of patient cells were not performed.
In 3 patients from a large consanguineous Saudi Arabian family (family 6) with severe congenital liver disease (SCOLIV; 619991), Moreno Traspas et al. (2022) identified a homozygous 1-bp deletion (c.4343delT) in exon 39 of the FOCAD gene, predicted to result in a frameshift and premature termination (Leu1448CysfsTer3) in the DUF3028 domain. The mutation, which was found by exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the family. It was not present in the ExAC or gnomAD databases. Functional studies of the variant and studies of patient cells were not performed, but it was predicted to result in a loss of function. Two of the patients died in the first year of life.
Brockschmidt, A., Trost, D., Peterziel, H., Zimmermann, K., Ehrler, M., Grassmann, H., Pfenning, P.-N., Waha, A., Wohlleber, D., Brockschmidt, F. F., Jugold, M., Hoischen, A., and 10 others. KIAA1797/FOCAD encodes a novel focal adhesion protein with tumour suppressor function in gliomas. Brain 135: 1027-1041, 2012. [PubMed: 22427331] [Full Text: https://doi.org/10.1093/brain/aws045]
MacFarland, S. P., Xie, H., Dent, M. H., Greed, B., Plon, S. E., Scollon, S. R., Brodeur, G. M., Howe, J. R. FOCAD indel in a family with juvenile polyposis syndrome. J. Pediat. Gastroent. Nutr. 75: 56-58, 2022. [PubMed: 35622075] [Full Text: https://doi.org/10.1097/MPG.0000000000003470]
Melton, P. E., Rutherford, S., Voruganti, V. S., Goring, H. H. H., Laston, S., Haack, K., Comuzzie, A. G., Dyer, T. D., Johnson, M. P., Kent, J. W., Jr., Curran, J. E., Moses, E. K., and 13 others. Bivariate genetic association of KIAA1797 with heart rate in American Indians: the Strong Heart Family Study. Hum. Molec. Genet. 19: 3662-3671, 2010. [PubMed: 20601674] [Full Text: https://doi.org/10.1093/hmg/ddq274]
Moreno Traspas, R., Teoh, T. S., Wong, P.-M., Maier, M., Chia, C. Y., Lay, K., Ali, N. A., Larson, A., Al Mutairi, F., Al-Sannaa, N. A., Faqeih, E. A., Alfadhel, M., and 35 others. Loss of FOCAD, operating via the SKI messenger RNA surveillance pathway, causes a pediatric syndrome with liver cirrhosis. Nature Genet. 54: 1214-1226, 2022. [PubMed: 35864190] [Full Text: https://doi.org/10.1038/s41588-022-01120-0]
Nagase, T., Nakayama, M., Nakajima, D., Kikuno, R., Ohara, O. Prediction of the coding sequences of unidentified human genes. XX. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. DNA Res. 8: 85-95, 2001. [PubMed: 11347906] [Full Text: https://doi.org/10.1093/dnares/8.2.85]
Weren, R. D. A., Venkatachalam, R., Cazier, J.-B., Farin, H. F., Kets, C. M., de Voer, R. M., Vreede, L., Verwiel, E. T. P., van Asseldonk, M., Kamping, E. J., Kiemeney, L. A., Neveling, K., and 11 others. Germline deletions in the tumour suppressor gene FOCAD are associated with polyposis and colorectal cancer development. J. Path. 236: 155-64, 2015. [PubMed: 25712196] [Full Text: https://doi.org/10.1002/path.4520]