Two loss‐of‐function ANKRD11 variants in Chinese patients with short stature and a possible molecular pathway

Abstract

KBG syndrome is a rare genetic disease characterized mainly by skeletal abnormalities, distinctive facial features, and intellectual disability. Heterozygous mutations in ANKRD11 gene, or deletion of 16q24.3 that includes ANKRD11 gene are the cause of KBG syndrome. We describe two patients presenting with short stature and partial facial features, whereas no intellectual disability or hearing loss was observed in them. Two ANKRD11 variants, c.4039_4041del (p. Lys1347del) and c.6427C > G (p. Leu2143Val), were identified in this study. Both of them were classified as variants of uncertain significance (VOUS) by ACMG/AMP guidelines and were inherited from their mothers. ANKRD11 could enhance the transactivation of p21 gene, which was identified to participate in chondrogenic differentiation. In this study, we demonstrated that the knockdown of ANKRD11 could reduce the p21‐promoter luciferase activities while re‐introduction of wild type ANKRD11, but not ANKRD11 variants (p. Lys1347del or p. Leu2143Val), could restore the p21 levels. Thus, our study report two loss‐of‐function ANKRD11 variants which might provide new insight on pathogenic mechanism that correlates ANKRD11 variants with the short stature phenotype of KBG syndrome.

Missense variants in ANKRD11 cause KBG syndrome by impairment of stability or transcriptional activity of the encoded protein

“…In contrast, the only other variant with altered proteasome degradation, p.(Arg2585Cys), showed reduced proteasome degradation, and might slightly increase protein stability, although the latter was not statistically significant. The p.(Arg2585Cys) variant is also the only tested variant that resulted in reduced transcriptional repression on CDKN1A/P21 , consistent with previous observations for p.(Leu2143Val) [14]. These findings suggest that p.(Arg2585Cys) results in loss-of-function, despite a potential accumulation of mutant ANKRD11 that contrasts with the dosage reduction seen for the other tested variants.…”

“…This is supported by observations of reduced amounts of ANKRD11 mRNA and protein when the gene contains a PTV [12], suggesting that variants trigger the nonsense-mediated decay (NMD) pathway [12], although PTVs leading to a (partial) escape from NMD have also been described [7, 13]. Also consistent with haploinsufficiency is the finding that ANKRD11 mutated with p.(Lys1347del) or p.(Leu2143Val) shows reduced transcriptional activity on the p21 promotor in cell-based systems, and that this effect can be rescued by wildtype but not mutated ANKRD11 [14].…”

“…In the literature, ∼2.6% of ( de novo ) variants in ANKRD11 are missense variants [19], listed in Table S1. Missense variants are reported with varying levels of evidence on pathogenicity, and functional studies have only been performed for p.(Leu2143Val), showing a loss-of-function effect [14]. The Yoda mutant mouse (C3H.Cg-Ankrd11Yod/H, p.(Glu2502Lys)), carries an Ankrd11 missense variant and shows phenotypic overlap with core features of KBG syndrome, including reduced body size as well as craniofacial abnormalities such as shortened snouts with deformed nasal bones, wider skulls and failure of cranial sutures to close [20].…”

Genetic and Phenotypic Spectrum of KBG Syndrome: A Report of 13 New Chinese Cases and a Review of the Literature

“…The flow chart of the selected patients is shown in Figure 2 A. Only the KBGS patients with ANKRD11 gene variation were included ( n = 253) [ 2 , 5 , 8 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 ]. The types of variations included frameshift variation ( n = 158), nonsense variation ( n = 61), copy number variation ( n = 13), missense variation ( n = 13), splice site variation ( n = 6), and deletion variation ( n = 2).…”

“…The pathogenicity of a missense variation in the ANKRD11 gene needs to be considered cautiously; clinical phenotypes caused by other genes need to be excluded, and functional verification may be necessary. Zhang et al [ 50 ] found that a missense variation, c. 6427C > G (p.L2143V), in the ANKRD11 gene did not lead to abnormal expression of ANKRD11 protein and RNA, but could not restore the regulatory effect of P21 , which is an important factor in regulating cartilage differentiation. At present, only 13 cases of KBGS caused by missense variation of the ANKRD11 gene have been reported.…”