Sequencing of a KLK15 gene variant in a large cohort of hypermobile Ehlers- Danlos syndrome patients
Laboratory Genetics and Genomics
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Primary Categories:
- Laboratory Genetics
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Secondary Categories:
- Laboratory Genetics
Introduction:
Ehlers- Danlos syndrome (EDS) is the most common inherited genetic connective tissue disorder (CTD), characterized by generalized joint hypermobility, chronic pain, subluxations/dislocations, along with a plethora of additional debilitating signs and symptoms in multiple systems. Given the overlapping features of many of the genetic CTDs, gene panel testing examining multiple genes is standard and often requested to at least rule out the vascular disorders. Although genetic testing has uncovered the etiology of the majority of EDS subtypes, the etiology of hypermobility EDS (hEDS), that is estimated to account for 90% of EDS, remains elusive.
Exome and genome sequencing to date has not discovered a common etiology. Recently, Gensemer et al (2024) reported a shared variant in the Kallikrein gene 15 (KLK15) identified in a large and small family with hEDS. The Center for Human Genetics specializes in providing diagnostic evaluation, management, genetic counseling, and genetic testing for EDS and other genetic CTDs. Many of our patients asked to be tested for the KLK15 gene variant after the aforementioned study was released. Hence, research sequencing of the reported KLK15 gene variant was performed in a large cohort of hEDS patients evaluated and tested at our Center.
Methods:
All patients in this study were seen by clinical Geneticists at the Center for Human Genetics and were referred for a CTD evaluation. The patients were classified as having hEDS according to the 2017 nosology following negative Connect2 testing of 42 CTD genes that included COL1A1, COL1A2, COL3A1, COL5A1, COL5A2, SMAD3, SMAD2, TGFBR1, TGFBR2, TGFB2 and TGFB3.
268 DNA samples were sequenced for KLK15 exon 4 in the region harboring the KLK15:Gly226Asp (NM_017509.4) variant. The primer design (Gensemer et al) was used with the exception that M13 tags were added and Sanger sequencing was conducted with M13 primers.
Results:
Out of the 268 samples, one was found to be heterozygous for the KLK15:Gly226Asp variant (Northern European ancestry). Her father (historical hypermobility, osteoarthritis, chronic pain , and subluxations) was also found to harbor the variant. The proband was re-evaluated clinically and her affected sister was newly evaluated. Both were found to meet hEDS criteria and have current Beighton scores of 6 (historical 9). The variant was absent from the affected sister, suggesting that the presence of the variant does not correlate with hEDS in this family.
The KLK15:Gly226Asp variant frequency is approximately 0.00246 (~1/406) and is primarily found in Americans of European descent (dbSNP). Thus, out of 268 samples, 1 to 2 patients would be expected to be positive by chance.
Conclusion:
While the KLK15 variant was found to correlate with hEDS in the 1 large and 1 small family reported by Gensemer et al.,and the variant is predicted to be damaging by Polyphen and SIFT, we found in our large cohort of hEDS patients that the frequency of the KLK15:Gly226Asp variant does not differ significantly from the expected population frequency and more importantly does not segregate with the hEDS in the family reported here.
Ehlers- Danlos syndrome (EDS) is the most common inherited genetic connective tissue disorder (CTD), characterized by generalized joint hypermobility, chronic pain, subluxations/dislocations, along with a plethora of additional debilitating signs and symptoms in multiple systems. Given the overlapping features of many of the genetic CTDs, gene panel testing examining multiple genes is standard and often requested to at least rule out the vascular disorders. Although genetic testing has uncovered the etiology of the majority of EDS subtypes, the etiology of hypermobility EDS (hEDS), that is estimated to account for 90% of EDS, remains elusive.
Exome and genome sequencing to date has not discovered a common etiology. Recently, Gensemer et al (2024) reported a shared variant in the Kallikrein gene 15 (KLK15) identified in a large and small family with hEDS. The Center for Human Genetics specializes in providing diagnostic evaluation, management, genetic counseling, and genetic testing for EDS and other genetic CTDs. Many of our patients asked to be tested for the KLK15 gene variant after the aforementioned study was released. Hence, research sequencing of the reported KLK15 gene variant was performed in a large cohort of hEDS patients evaluated and tested at our Center.
Methods:
All patients in this study were seen by clinical Geneticists at the Center for Human Genetics and were referred for a CTD evaluation. The patients were classified as having hEDS according to the 2017 nosology following negative Connect2 testing of 42 CTD genes that included COL1A1, COL1A2, COL3A1, COL5A1, COL5A2, SMAD3, SMAD2, TGFBR1, TGFBR2, TGFB2 and TGFB3.
268 DNA samples were sequenced for KLK15 exon 4 in the region harboring the KLK15:Gly226Asp (NM_017509.4) variant. The primer design (Gensemer et al) was used with the exception that M13 tags were added and Sanger sequencing was conducted with M13 primers.
Results:
Out of the 268 samples, one was found to be heterozygous for the KLK15:Gly226Asp variant (Northern European ancestry). Her father (historical hypermobility, osteoarthritis, chronic pain , and subluxations) was also found to harbor the variant. The proband was re-evaluated clinically and her affected sister was newly evaluated. Both were found to meet hEDS criteria and have current Beighton scores of 6 (historical 9). The variant was absent from the affected sister, suggesting that the presence of the variant does not correlate with hEDS in this family.
The KLK15:Gly226Asp variant frequency is approximately 0.00246 (~1/406) and is primarily found in Americans of European descent (dbSNP). Thus, out of 268 samples, 1 to 2 patients would be expected to be positive by chance.
Conclusion:
While the KLK15 variant was found to correlate with hEDS in the 1 large and 1 small family reported by Gensemer et al.,and the variant is predicted to be damaging by Polyphen and SIFT, we found in our large cohort of hEDS patients that the frequency of the KLK15:Gly226Asp variant does not differ significantly from the expected population frequency and more importantly does not segregate with the hEDS in the family reported here.