A Short stature and mesomelic shortening of arms in the patient. B–E Skeletal X-ray surveys of the patient's right upper extremity (B), lower extremities (C), anterior view of the lower spine and pelvis (D), and lateral view of the lower spine and pelvis (E)

Genetic results of the family. A Homozygous intervals in the patient’s genome, as determined by HomozygosityMapper. MSGN1 resides in a ~ 13.2 Mb homozygous interval on chromosome 2 (black arrow). B Sanger sequencing electropherogram of the patient’s variant in MSGN1. The mutated base is indicated by a black arrow. C Segregation of the MSGN1 variant within the family

In vitro transfection of HEK 293T cells with CMV:MSGN1 (WT)-FLAG-tag and CMV:MSGN1 p.(Arg125Leu)-FLAG-tag plasmids at different concentrations. A Immunofluorescence showing expression of tagged MSGN1 proteins (WT) or p.(Arg125Leu) after 48h of transfection. Corresponding experimental controls are shown in Additional file 4: Fig. S3A. B Quantification of MSGN1 localization in transfected cells. Fluorescence signals in a by single z-plane were visualized by confocal laser-scanning microscopy and subsequently signal intensity was measured in single cells (cyto: cytoplasm; nuc: nucleus) and outside of cells (bg: background). Graphs show signal intensity measurements of the RFP channel (MSGN1 Flag-Tag) of 30 cells per experimental group and 30 background positions. Signal intensity measurements of the corresponding DAPI channel for nucleus identification are given in Additional file 4: Fig S3B. Values are given in Additional file 1: Excel file S1

In situ hybridization images of tbxta (no tail, Brachyury) expression in uninjected wild-type controls (A), wild-type msgn1 RNA (B) and mutant msgn1 RNA p.(Arg71Leu) in zebrafish (≈ p.(Arg125Leu) in humans) injected embryos (C). D Quantification of tbxta ISH signal in posterior PSM cells (orange ROI mark) is shown by normalized intensity comparison between the three groups of three independent experiments (WT (uninjected): 49 embryos; + msgn1 (WT) RNA: 58 embryos; + msgn1 p.(Arg71Leu) RNA: 54 embryos). Mosaic transient-transgenic overexpression of wild-type msgn1 results in partial disruption of Notch signals in PSM cells (E) and influences normal notochord (marked with dashed lines) and pectoral fin bud development (marked with arrow). F In vivo images show representative embryos of three independent injections experiments (overall: 37 imaged embryos; WT: 5 embryos; + msgn1 mosaic: 32 embryos). ISH signal quantification values and injection statistics are given in Additional file 1: Excel file S1

A In situ hybridization images of tbx6 (tbx6r/fss/fussed somites/tbx24) and tbx16 (spt/spatetail) expression in injected embryos 19 hpf showing mosaic transient-transgenic overexpression of wild-type msgn1. Expression of tbx6 and tbx16 was detected in PSM cells (endogenous expression) and within the trunk, colocalizing with notochord alterations (shown in higher magnification). B In 30 hpf old msgn1 mosaic embryos, ectopic expression of bmp2a was detected in the head region, consistent with strong ectopic msgn1 expression in trunk and head regions of injected embryos at this stage