Targeted sequencing of FH-deficient uterine leiomyomas reveals biallelic inactivating somatic fumarase variants and allows characterization of missense variants

Abstract

Uterine leiomyomas (ULs) constitute a considerable health burden in the general female population. The fumarate hydratase (FH) deficient subtype is found in up to 1.6% and can occur in hereditary leiomyomatosis and renal cell carcinoma (HLRCC) syndrome. We sequenced 13 FH deficient ULs from a previous immunohistochemical screen using a targeted panel and identified biallelic FH variants in all. In eight, we found an FH point mutation (two truncating, six missense) with evidence for loss of the second allele. Variant allele-frequencies in all cases with a point mutation pointed to somatic variants. Spatial clustering of the identified missense variants in the lyase domain indicated altered fumarase oligomerization with subsequent degradation as explanation for the observed FH deficiency. Biallelic FH deletions in five tumors confirm the importance of copy number loss as mutational mechanism. By curating all pathogenic FH variants and calculating their population frequency, we estimate a carrier frequency of up to 1/2,563. Comparing with the prevalence of FH deficient ULs, we conclude that most are sporadic and estimate 2.7–13.9% of females with an FH deficient UL to carry a germline FH variant. Further prospective tumor/normal sequencing studies are needed to develop a reliable screening strategy for HLRCC in women with ULs.

Fumarate hydratase variant prevalence and manifestations among individuals receiving germline testing

“…By examining these variants in publicly available databases, the authors estimated carrier frequencies of 1 in 2563 (BRAVO database) and 1 in 3247 (gnomAD database). 18 Such estimates continue to confirm that the frequency of HLRCC is magnitudes higher than previously suggested. 6,7 In fact, HLRCC may be the most common hereditary kidney cancer syndrome with a higher prevalence than von Hippel-Lindau syndrome (1 in 36,000) and Birt-Hogg-Dubé syndrome (1 in 200,000).…”

Comprehensive Review of Uterine Fibroids: Developmental Origin, Pathogenesis, and Treatment

“…Similar to the FH deficiency subtype, COL4A5/COL4A6 deletions are a rare subtype constituting about 2% of uterine fibroids ( 193 ). Integrated data analysis reveals insulin receptor substrate-4 ( IRS4 ), a gene located adjacent to COL4A5 , as the most uniquely expressed gene in this uterine fibroid subtype ( 189 ).…”

Prenatal phenotype of PNKP-related primary microcephaly associated with variants affecting both the FHA and phosphatase domain

“…AA positions 20, 441, and 462 are labeled for orientation. In the panel below, a generalized additive model shows the CADD values for all possible missense variants (red horizontal line = recommended cut-off [ 20 ]). Additional boxes show the affected regions of the in-frame deletions resulting from the synonymous variant c.498G>A in orange or the splicing variant c.1029+2T>C in pink.…”

“… A Schematic depiction of the PNKP protein with FHA in blue, Phosphatase and kinase domain in green and linker region in gray (based on Uniprot Q96T60 and [ 20 ]). Disease-associated missense variants are displayed toward the top, red shapes show (likely) pathogenic variants, yellow shapes show variants of unknown significance, and gray shapes show (likely) benign variants.…”

“…In brief, reads were demultiplexed, adapters trimmed, and overrepresented sequences removed before we aligned the reads to the hg38 reference. Alignments were visualized and inspected for aberrant splicing as described previously [ 20 ]. We applied iREAD [ 21 ] to quantify observed intron retention events.…”