Ectodermal dysplasia (ED) syndromes are a heterogeneous group of disorders that are characterized by congenital defects in two or more ectodermal structures. Among these structures, at least one must involve the hair, teeth, nails, or sweat glands (1,2). ED may also impact the skin, eye (lens or retina), inner ear, development of fingers and toes, nerves and other body parts (2). At least 150 different types of ED have been observed (2). EDs are classified in subgroups according to the presence or absence of the four primary defects observed in ED: Trichodysplasia (hair dysplasia), dental dysplasia, onychodysplasia (nail dysplasia), dyshidrosis (sweat gland dysplasia) (2).

A rare type of ED, ED-12 is described by congenital absent teeth, dystrophic toenails, hypohidrosis, and hair abnormalities and is linked to mutations in the keratinocyte differentiation factor 1 (KDF1) gene (3). Additionally, KDF1 is the most recently identified rare candidate gene for tooth agenesis (4). This gene is essential for skin epidermal differentiation and it is known that KDF1 deficiency results in significant abnormalities in skin development (5). However, the exact role and importance of KDF1 is still not entirely known (5).

In the present study, a case of a three-generation family was described where the novel mutation c.812A>C (p.Lys271Thr or K271T) in KDF1 was identified in four family members. The family was referred to the Clinical Laboratory Genetics, Access to Genome P.C. (Athens, Greece), after the birth of their first child that presented with natal teeth. Following the detection of the novel KDF1 mutation, further testing was performed in other family members and it was revealed that the father and paternal grandfather of the child were also carriers of the same mutation. Moreover, the second child of the family that was born 2 years later, was also born with natal teeth and was a carrier of the same mutation. This is an extremely rare case of the presence of natal teeth in carriers of a KDF1 mutation, since only 2 cases have been described thus far (3,6).

The family was referred to Clinical Laboratory Genetics, Access to Genome P.C., after a newborn presented with 12 natal teeth at birth (III-1) (Fig. 1). Whole exome sequencing (WES) was performed using next generation sequencing [accession no. ERR14252058; European Nucleotide Archive (ENA)]. DNA was isolated from the newborn's whole blood cells. Exome amplification was performed using Ion AmpliSeq^™ Exome RDY (cat. no. A38264; Thermo Fisher Scientific, Inc.). Nucleotide Sequencing was performed using Ion Chef Instrument and Ion GeneStudio^™ S5 System (Thermo Fisher Scientific, Inc.). The analysis involved 4,431 genes that are associated with known genetic diseases and syndromes. Alamut^® Visual (version 1.7.1; SOPHiA GENETICS SAS) and Varsome Clinical (V.9.2.2; Saphetor SA) bioinformatic analysis systems were used for the data analysis. All findings from the analysis above were evaluated according to the American College of Medical Genetics and Genomics guidelines as well as the international scientific literature (7). The reference genome that was used is UCSC hg19. Bioinformatic analysis revealed a novel mutation in KDF1, namely c.812A>C (p.Lys271Thr or K271T).

In order to confirm the presence of the mutation, Sanger sequencing was performed in the patient. Following DNA amplification by PCR, part of the KDF1 gene was sequenced and was compared with the control sequence. The sequences of the primers used were forward, 5'-CCACAGTGACTAAAGACCCCATTCC-3' and reverse, 5'-TCGTGGCTCCGAGGAGTACTAT-3'. The results confirmed the presence of the novel c.812A>C mutation in KDF1.

Sanger sequencing of KDF1 was performed on parental DNA, isolated from whole blood cells, in order to determine if the mutation was inherited or if it occurred de novo. Sequencing analysis revealed that the father of the patient (II-1) was also a carrier of the same mutation, indicating that the c.812A>C mutation was inherited. The paternal grandfather (I-1) and the second child (III-2) of the family, born 2 years later, were also tested and the results confirmed that they are carriers of the c.812A>C mutation in KDF1 (Fig. 2).

Mutations in KDF1 are associated with the manifestation of clinical characteristics of ED-12 (hypohidrotic/hair/tooth/nail type, Phenotype MIM no. 617337; OMIM^®, John Hopkins University, Baltimore, USA) following autosomal dominant mode of inheritance. In the present study, a case of a family with a familial, previously undescribed mutation in KDF1, present in four family members and three generations is described. All carrier members exhibited clinical manifestations of ED. The novel mutation is a missense mutation that has not been reported in the ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/) and Decipher (https://www.deciphergenomics.org/) databases and is not described in the international literature. Bioinformatic analysis suggested that the mutation likely affects the structure and function of the KDF1 protein and according to the ACMG/AMP guidelines, it is categorized as a variant of unknown significance based on the PM2, PP2, PP3 criteria (7).

In 2013, KDF1 was first described by Lee et al (8). They described a Kdf1 mouse mutant that had a short snout and short limbs. This gene was expressed in epidermal cells during epidermal development. The Kdf1 mouse mutant showed a thickened epidermis and defective epidermal barrier formation due to keratinocyte defects. Zeng et al (9) showed that KDF1 is also expressed in tooth germs during tooth development, indicating that KDF1 plays an important role during tooth germ development (9).

To date, only a few cases of KDF1 mutations have been reported and the phenotype associated with the mutations varies (Table II). A heterozygous KDF1 mutation was first reported to cause ED-12 (autosomal dominant hypohidrotic ED) by Shamseldin et al (3). In their study, they described the case of a multi-generational family with ED, where the affected members exhibited tooth agenesis, hypohidrosis, lusterless hair, dystrophic toenails, lateral thinning of eyebrows and keratosis pilaris (3). Only one of the patients had natal teeth. Another case of a newborn with natal teeth was described by Aljohar et al (6). This was the first case of multiple teeth present at birth due to a KDF1 mutation (6). ED due to a KDF1 mutation has also been described by Manaspon et al (10). They identified a novel de novo mutation in KDF1 in a 5-year-old patient with ED. Moreover, Kamat et al (11) described a patient with hypohidrotic ED that had peg-shaped teeth due to the presence of a novel mutation in KDF1.

As aforementioned, KDF1 is the most recently identified rare candidate gene for tooth agenesis. Zeng et al (9) described the case of a 7-year-old patient with non-syndromic tooth agenesis (NSTA) that had invaginated lingual fossa and high susceptibility to dental caries. The patient was found to be a carrier of a novel KDF1 mutation. Yu et al (4) have also described a case of NSTA in a patient carrying a novel KDF1 mutation. In the present case report, the novel KDF1 mutation led to the presence of natal teeth in all carriers. Thus far, only 2 cases of KDF1 mutations leading to natal teeth at birth have been reported (3,6). To the best of our knowledge, this was the third instance of the presence of natal teeth at birth due to a KDF1 mutation. The presence of natal teeth in newborns with ED is highly uncommon (6).

As Zeng et al (9) suggested, the phenotype differences between patients with KDF1 mutations may be due to the different mutations or the difference in genetic background of the patients. In the present case report, all affected family members that were reported were born with natal teeth. Moreover, both adult members that are carriers of the mutation now have hypodontia. However, dystrophic toenails and atopic dermatitis are present in two out of the four affected members.

In the present study, the case of four family members across three generations who are carriers of the previously unreported c.812A>C mutation in KDF1 were described. The present case report included the clinical manifestations of all carrier members. Notably, all four affected family members had natal teeth at birth and to the best of our knowledge, this was the third report of natal teeth at birth due to a KDF1 mutation. The findings of the present case report are significant for establishing genotype-phenotype associations related to KDF1 mutations. Furthermore, they are crucial for genetic counseling, particularly in cases where this KDF1 mutation is detected prenatally.