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Other entities represented in this entry:
HGNC Approved Gene Symbol: TCF12
Cytogenetic location: 15q21.3 Genomic coordinates (GRCh38) : 15:56,918,090-57,291,310 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 15q21.3 | Craniosynostosis 3 | 615314 | Autosomal dominant | 3 |
| Hypogonadotropic hypogonadism 26 with or without anosmia | 619718 | Autosomal dominant; Autosomal recessive | 3 |
Zhang et al. (1991) obtained a partial cDNA for HTF4 which predicted a protein that is a member of the class A basic helix-loop-helix (bHLH) family. The same cDNA, designated HEB, was cloned by Hu et al. (1992).
Gan et al. (2002) identified 3 TCF12 variants that result from alternative splicing and differential exon utilization. Two of the variants differ in the 5-prime untranslated region but encode identical proteins.
Wang et al. (2006) noted that E2A (TCF3; 147141) homodimers are essential for early B-cell development, whereas HEB/E2A heterodimers are dominant during T-cell development. By screening a mouse pro-T-cell cDNA library, followed by database analysis, they identified a novel HEB variant, which they termed HEBAlt. HEBAlt includes the bHLH domain and activation domain-2 (AD2) of canonical HEB (HEBCan), but it replaces AD1 with an alternative domain homologous to the N-terminal region of the ITF2A variant of ITF2 (TCF4; 602272). The alternative domain of HEBAlt is well conserved in vertebrates. RT-PCR analysis showed that HebAlt was expressed only in the double-negative stages of mouse thymocyte development.
Gan et al. (2002) determined that the TCF12 gene contains 21 exons and spans about 370 kb.
Zhang et al. (1995) used a panel of somatic cell hybrids to map HTF4 to chromosome 15. By fluorescence in situ hybridization, they further localized the gene to 15q21.
TCF12/NR4A3 Fusion Gene
By spectral karyotyping, Sjogren et al. (2000) identified a reciprocal t(9;15)(q22;q21) translocation in cells obtained from a tumor with characteristics of extraskeletal myxoid chondrosarcoma (612237). The translocation produced a chimeric transcript encoding a protein in which the first 108 amino acids of the N terminus of TCF12 were fused in-frame upstream of the entire NR4A3 (600542) sequence. The N-terminal TCF12 sequence included in the fusion product contains potential phosphorylation and N-glycosylation sites. Gan et al. (2002) determined that intron 5 of the TCF12 gene was the region involved in the translocation.
Based on studies of the mouse and chicken cDNAs, Zhang and Bina (1992) proposed that transcripts of HTF4 can be differentially spliced to yield distinct but related proteins which are evolutionarily similar to the products of the E2A gene. In vitro assays had shown that HTF4 can form heterodimers with other bHLH proteins of class A (e.g., the E2A proteins; see 147141) and class B (e.g., the myogenic factors; MYF3, 159970; MYF5, 159990; and MYF6, 159991), as well as the inhibitor of DNA binding (ID1; 600349) and stem cell leukemia hematopoietic transcription factor (TAL1; 187040).
In DNA binding assays, (Doyle et al., 1994) found that complexes of HTF4 with the myogenic factors have a relatively high affinity for the E box motifs of the mE2 (CACGTG) and kappa E2/muE5 (CACCTG) types, whereas heterodimers of HTF4 and TAL1 interact poorly. They suggested that these results and those obtained from transient expression studies indicated that leukemogenesis caused by TAL1 might include a pathway where TAL1 would act as a negative regulator of gene expression by forming a complex with class A bHLH proteins.
By Northern blot analysis, Zhang et al. (1995) showed that TCF12 is expressed at varying levels in many human cell lines and tissues. High levels of transcription in Jurkat cells supported the view that TCF12 gene products may play a central role in T-cell regulation (Hu et al., 1992; Sawada and Littman, 1993; Doyle et al., 1994), and detection of the mRNA in human heart and skeletal muscle supported a role for TCF12 in myogenesis.
Wang et al. (2006) found that HEBAlt specifically bound to an E box motif. HEBAlt mRNA was upregulated synergistically by HEBCan activity and Delta (see 606582)-Notch (see 190198) signaling. Further experiments demonstrated that HEBAlt and HEBCan are functionally distinct transcription factors, with HEBAlt specifically required for efficient generation of early T-cell precursors.
Goardon et al. (2006) found that ETO2 (CBFA2T3; 603870) copurified with TAL1 complexes in human and mouse erythroleukemia cells. Protein pull-down assays revealed that ETO2 interacted with E2A and HEB within the TAL1 complex, but not with TAL1 itself. ETO2 also interacted with E2A in erythroid cells independent of the TAL1 complex. Reporter gene assays revealed that ETO2 repressed the transcriptional activity of the complex. The ETO2 content in TAL1 complexes was high during the proliferative phase in erythroid cells. In contrast, ETO2 was downregulated upon terminal differentiation, concomitant with appearance of histone modifications associated with gene activation and expression of glycophorin A (GPA; 617922) and band 4.2 (EPB42; 177070), which are markers of erythrocyte maturation. Knockdown of ETO2 via small interfering RNA induced growth arrest and differentiation in human and mouse erythroid progenitors. Goardon et al. (2006) concluded that ETO2 is required for expansion of erythroid progenitors, but that it is dispensable for terminal maturation. They proposed that the stoichiometry of ETO2 with the TAL1 complex controls the transition from erythroid progenitor expansion to terminal differentiation.
Craniosynostosis 3
By exome sequencing of 347 DNA samples from unrelated individuals with craniosynostosis (CRS3; 615314), Sharma et al. (2013) identified heterozygosity for 36 different mutations in the TCF12 gene (see, e.g., 600480.0001-600480.0007) in 38 families. The mutations occurred predominantly in patients with coronal synostosis, accounting for 32% and 10% of individuals with bilateral and unilateral pathology, respectively; 2 patients had both coronal and sagittal synostosis and 2 patients had only sagittal synostosis. In 36 families tested, the TCF12 mutation was shown to have arisen de novo. In 23 families, cascade testing identified 34 additional mutation-positive individuals, only 16 of whom had craniosynostosis or other relevant features, indicating substantial (53%) nonpenetrance. The mutations identified in TCF12 included 15 frameshift, 14 nonsense, 7 splicing, and 2 missense changes, suggesting a loss-of-function mechanism. All but 1 were located between exons 10 and 19; no genotype-phenotype correlation was detected.
In a cohort of 182 Spanish probands with craniosynostosis, Paumard-Hernandez et al. (2015) screened 7 craniosynostosis-associated genes and identified 5 patients with coronal or multisutural involvement who had mutations in the TCF12 gene (see, e.g., 600480.0001 and 600480.0008). The authors noted that 4 of the 5 Spanish probands were initially referred for Saethre-Chotzen syndrome (SCS; 101400) and 1 for Muenke syndrome (MNKES; 602849).
Hypogonadotropic Hypogonadism 26
In 13 patients from 12 families with hypogonadotropic hypogonadism with anosmia (HH26; 619718), Davis et al. (2020) identified heterozygosity for frameshift or splice-site mutations in the TCF12 gene (see, e.g., 600480.0002 and 600480.0009-600480.0011). The mutations were confirmed by Sanger sequencing and segregated with incomplete penetrance in the 5 families for which data was available; none was found in public variant databases. Craniosynostosis was present in 3 of the families, including in 1 of the probands (see 600480.0011). Using GeneMatcher, the authors also identified a consanguineous Pakistani family in which the proband exhibited bilateral coronal synostosis as well as hypogonadotropic hypogonadism; he was homozygous for a 1-bp deletion in TCF12 (600480.0012) for which his unaffected parents were heterozygous.
Using targeted morpholino injections, Davis et al. (2020) transiently suppressed tcf12 in zebrafish larvae. Immunostaining of larval batches at 2 days postfertilization (dpf) revealed a dose-dependent significant reduction in the length of the terminal nerve axons, which provide the scaffold for migrating GnRH neurons towards the hypothalamus. In addition, there was a significant reduction in the size of the olfactory bulb. Coinjection of human wildtype TCF12 resulted in significant restoration of terminal nerve axon length and olfactory bulb size in 2-dpf larvae. Analysis of morpholino-injected GnRH3 GFP transgenic zebrafish embryos showed GnRH3 reporter cell disorganization, including dispersed localization of individual cells and unilateral asymmetry. Quantification of the area marked by GPF, a proxy for the number of GnRH neurons, showed a significant reduction in morphants versus controls. CRISPR/Cas9-mediated genome editing of the tcf12 locus in GnRH3 GFP transgenic zebrafish confirmed the findings. The authors also observed that tcf12 morphants or mutants showed attenuation of the orthologous expression of tcf3a/b (TCF3; 147141), encoding a binding partner of TCF12, and stub1 (607207), a gene that is associated with a syndromic form of HH and that also maps to a TCF12 affinity network. Expression of STUB1 was sufficient to significantly rescue tcf12-induced GnRH neuronal patterning defects. The authors concluded that tcf12 is involved in the GnRH axis development in zebrafish and likely plays a role in patterning of GNRH3 neurons as well as in regulating expression of multiple genes involved in the establishment of the GnRH axis.
In a father and son and an unrelated man with craniosynostosis (CRS3; 615314), Sharma et al. (2013) identified heterozygosity for a c.842C-G transversion (c.842C-G, VAR NM_207040.1) in exon 11 of the TCF12 gene, resulting in a ser281-to-ter (S281X) substitution. The mutation arose de novo in the sporadic case. The father had left coronal synostosis whereas his son had right coronal synostosis, and the unrelated man had bicoronal craniosynostosis. Additional features included corneal abnormalities in the father and a small mass near the pineal gland in the son; the sporadic patient had low anterior hairline, incomplete descent of testes, mild learning disabilities, and mild ventriculomegaly, and also required an additional surgical procedure to correct supraorbital retrusion. Sharma et al. (2013) noted that the son and the sporadic patient had previously been given a clinical diagnosis of Saethre-Chotzen syndrome (SCS; 101400).
In a Spanish proband (patient 2) with plagiocephaly resulting from synostosis of the left coronal suture, Paumard-Hernandez et al. (2015) identified heterozygosity for the S281X substitution in the TCF12 gene. The mutation was not found in the unaffected parents or unaffected brother. Other features in the proband included flat and asymmetric face, autism, delayed language, and bilateral sensorineural hearing loss. Brain MRI showed lateral ventricular asymmetry. The patient had initially been given a clinical diagnosis of SCS.
Craniosynostosis 3
In the male probands from 2 unrelated families with craniosynostosis (CRS3; 615314), Sharma et al. (2013) identified heterozygosity for a 1-bp duplication (c.1491dupT, NM_207040.1) in exon 17 of the TCF12 gene, causing a frameshift predicted to result in a premature termination codon (Val498CysfsTer12). One proband had bicoronal synostosis, whereas the other had right coronal synostosis; they inherited the mutation from their unaffected father and mother, respectively. RT-PCR of mRNA from patient blood samples showed lower expression of the mutant allele compared to wildtype, consistent with nonsense-mediated decay; the mutant-to-wildtype allele ratio was lower in the affected individuals than in the unaffected carriers. Additional features in the proband with bicoronal synostosis included dental crowding, bilateral transverse palmar creases, and hallux valgus; the other proband was tall and also had a right transverse palmar crease, flat thumbs, hallux valgus, and vertical strabismus, and he required an additional surgical procedure at 18 years of age. Brain scan was normal in both probands.
Hypogonadotropic Hypogonadism 26 with Anosmia
In a 32-year-old man (family III) with hypogonadotropic hypogonadism and anosmia (HH26; 619718), Davis et al. (2020) identified heterozygosity for the c.1491dup mutation in the TCF12 gene. The duplication was inherited from his father, who had only anosmia; the variant was not found in his unaffected mother or brother, or in public variant databases. Analysis of transcript levels in proband lymphoblastoid cell lines (LCLs) revealed a significant reduction of TCF12 mRNA; the results were validated by immunoblotting whole-cell protein lysates from the same LCLs, which showed a similar reduction in wildtype protein compared to control. Blot image signal enhancement revealed only trace amounts of truncated protein in the expected size.
In 2 cousins with craniosynostosis (CRS3; 615314), Sharma et al. (2013) identified heterozygosity for a c.722C-G transversion (c.722C-G, NM_207040.1) in exon 10 of the TCF12 gene, resulting in a ser241-to-ter (S241X) substitution. The 22-year-old female cousin had right coronal as well as sagittal synostosis, whereas the 27-year-old male cousin had only sagittal synostosis; the mutations were inherited from their unaffected mother and father, respectively. Both patients had mild learning disability. Other features in the woman included blepharoptosis requiring repair, strabismus, midface hypoplasia, class I dental malocclusion, brachydactyly, and camptodactyly of digits 3 and 5, and she required additional surgery for contour correction of the supraorbital rim and forehead. Other features in the man included partial sclerosis of both coronal sutures on plain radiography and a class II-1 malocclusion.
In a father and 2 sons with craniosynostosis (CRS3; 615314), Sharma et al. (2013) identified heterozygosity for a 1-bp deletion (c.1646delA, 207040.1) in exon 18 of the TCF12 gene, causing a frameshift predicted to result in a premature termination codon (Lys549ArgfsTer14). The 48-year-old father and his 9-year-old son had right coronal synostosis, whereas the 13-year-old son had sagittal synostosis. Brain scan in the 2 boys showed slightly enlarged lateral ventricles in both, as well as a Chiari I malformation in the older boy. Additional features in the father and older boy included bilateral transverse palmar creases and brachydactyly of the hands; the son was also diagnosed with Asperger syndrome. The younger son, who was autistic, also had deafness and relapsing respiratory tract infections.
In a 3.3-year-old boy with bicoronal and sagittal craniosynostosis (CRS3; 615314), Sharma et al. (2013) identified heterozygosity for a de novo c.1963G-T transversion (c.1963G-T, NM_207040.1) in exon 19 of the TCF12 gene, resulting in a glu655-to-ter (E655X) substitution. The mutation was not found in either parent. The patient had a normal brain scan and normal neurodevelopment, and no additional features were reported.
In a 3.6-year-old girl and her maternal aunt who had bicoronal craniosynostosis (CRS3; 615314), Sharma et al. (2013) identified heterozygosity for a G-C transversion (c.1035+3G-C, NM_207040.1) in intron 12 of the TCF12 gene, which was shown by RT-PCR of patient mRNA to cause skipping of exon 12. There was lower expression of the mutant allele compared to wildtype, consistent with nonsense-mediated decay. The mutation was also present in the girl's unaffected mother and maternal grandmother; the authors noted that there was relatively less skipped product present in blood samples from the affected girl than in her unaffected relatives. The affected girl had a normal brain scan and mild language delay, and she required further surgery 2 years after initial posterior release. Additional features in the affected aunt included mild brachydactyly of toes, severe early-onset rheumatoid arthritis, and Crohn disease, and she required speech therapy. The unaffected maternal grandmother also had rheumatoid arthritis; serum screening of the mother, aunt, and maternal grandmother showed normal indices of immune function. The 2 affected individuals had been clinically diagnosed with Saethre-Chotzen syndrome (101400), but no mutations were found in the TWIST1 gene (601622).
In a 14-year-old girl with bicoronal craniosynostosis and her affected mother, in whom the involved sutures were not determined (CRS3; 615314), Sharma et al. (2013) identified heterozygosity for a c.1912C-G transversion (c.1912C-G, NM_207040.1) in exon 19 of the TCF12 gene, resulting in a gln638-to-glu (Q638E) substitution at a highly conserved residue in the bHLH domain, a domain required for dimerization. In a transactivation assay, the combination of native TCF12 and TWIST proteins had a synergistic effect on activation relative to the activity of either protein alone; this effect was 65% lower with the Q638E mutation compared to wildtype. The daughter had a normal brain scan, and both affected individuals had normal neurodevelopment; the mother also had bilateral blepharoptosis, but no additional features were reported in the daughter.
In a Spanish child (patient 3) with turribrachycephaly due to bilateral coronal and left lambdoid suture synostosis (CRS3; 615314), Paumard-Hernandez et al. (2015) identified heterozygosity for a splice site mutation (c.826-2A-G, NM_207037.1) in intron 10 of the TCF12 gene. The mutation was not found in the proband's unaffected parents. Additional features in the proband included flat face, frontal asymmetry, hypertelorism, downslanting palpebral fissures, and dysmorphic ears. The authors noted that the patient was initially given a clinical diagnosis of Saethre-Chotzen syndrome (SCS; 101400).
In 2 male cousins (family I) with hypogonadotropic hypogonadism and anosmia (HH26; 619718), Davis et al. (2020) identified heterozygosity for a 1-bp duplication (c.1528dup, NM_207036.1) in exon 17 of the TCF12 gene, causing a frameshift predicted to result in a premature termination codon (Thr510AsnfsTer12). The duplication was also present in the apparently unaffected father of the proband and in the cousin's anosmic mother; it was not found in 5 other unaffected family members tested or in the dbSNP138, 1000 Genomes Project, NHLBI ESP, ExAC, and gnomAD databases. An uncle who was reported to have craniosynostosis was unavailable for clinical evaluation or DNA testing. Analysis of transcript levels in proband lymphoblastoid cell lines (LCLs) revealed a significant reduction of TCF12 mRNA; the results were validated by immunoblotting whole-cell protein lysates from the same LCLs, which showed a similar reduction in wildtype protein compared to control. Blot image signal enhancement revealed only trace amounts of truncated protein in the expected size.
In a male proband (family VII) with hypogonadotropic hypogonadism and anosmia (HH26; 619718), Davis et al. (2020) identified heterozygosity for a 1-bp duplication (c.1270dup, NM_207036.1) in exon 16 of the TCF12 gene, causing a frameshift predicted to result in a premature termination codon (Met424AsnfsTer10). The duplication was inherited from the proband's unaffected father and was also present in his brother, who had craniosynostosis but not HH; the mutation not found in public variant databases.
In a 19-year-old Spanish man (family XII) with hypogonadotropic hypogonadism and anosmia (HH26; 619718), Davis et al. (2020) identified heterozygosity for a de novo 1-bp duplication (c.596dup, NM_207036.1) in exon 9 of the TCF12 gene, causing a frameshift predicted to result in a premature termination codon (Asn200LysfsTer4). The patient, who also had plagiocephaly due to unilateral coronal synostosis, was originally reported as part of a craniosynostosis cohort by Paumard-Hernandez et al. (2015) (patient 1). The mutation was not found in his unaffected parents or brother, or in public variant databases.
In a 6-year-old Pakistani boy (family XIII) with hypogonadotropic hypogonadism (HH26; 619718), Davis et al. (2020) identified homozygosity for a 1-bp deletion (c.445del, NM_207036.1) in exon 7 of the TCF12 gene, causing a frameshift predicted to result in a premature termination codon (Ser149GlnfsTer96). The patient, who also had bilateral coronal suture synostosis, could not be tested for olfaction due to his young age and intellectual disability. His unaffected consanguineous parents were heterozygous for the deletion, which was not found in public variant databases.
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