Figure S1.
Expanded genetic and molecular analysis confirms complete loss-of-function ATRIP variant in patient F1Pt. (a) Photographs of patients F1Pt and F46.1 demonstrating facial similarities, including sloping forehead and beak-like nose. (b) Weight (Wgt), height (Hgt), and head circumference (occipital frontal circumference; OFC) at birth plotted as z-scores (SD from population mean for age and sex). Dashed line at −2 SD indicates cut-off for normal population distribution. ATRIP patients are denoted by red dots; previous reported ATR patients are denoted by blue dots. (c) Electropherograms of genomic DNA extracted from blood for F1Pt and a HC. Nucleotide numbering is in accordance with ENST00000320211.1. Images represent results from five independent experiments. (d) Population genetics: Highest SpliceAI Delta Score against gnomAD v4.0.0. allele frequency (AF) for splice region variants in ATRIP (ENST00000320211.1). Splice region variants are defined as nucleotide changes within the ±20 base pairs (bp) flanking the exon. Black dots and blue cross signs represent heterozygous and homozygous variants, respectively. More details regarding homozygous splice variants can be found in Table S4. Red shaded dots represent ATRIP variants of interest (c.829+5G>T and c.829+2T>G). (e) Fragment analysis and size profiles of PCR-amplified cDNA extracted from fibroblasts for F1Pt and a HC. Arrows indicate the position of forward and reverse primers used for PCR amplification. Percentages represent relative quantification of the 538 bp wild type (WT) and 380 bp mutant (r.7671_829del) fragment. Data are reflective of two independent experiments. (f) Electropherograms of cDNA extracted from PHA blasts for F1Fa (father), F1Mo (mother), and a HC. Nucleotide numbering is in accordance with ENST00000320211.1. Data are reflective of five independent experiments. (g) Sashimi plot of targeted RNA-seq data generated in Integrative Genomics Viewer. Input RNA was extracted from PHA blasts of F1Pt and a HC. Exon numbering is in accordance with ENST00000320211.1. (h) Fragment analysis of PCR-amplified cDNA using two primer pairs (S1: E3–E5; S2: E5–E7, indicated by arrows) on fibroblasts from F1Pt and a HC. Data are reflective of two independent experiments. (i) Reverse transcription quantitative PCR (RT-qPCR) analysis on fibroblasts of F1Pt and HCs (n = 3) of amplicon in exon 3–4 and exon 5–6. The relative expression to β-actin in a logarithmic scale is shown. Data from two independent experiments are shown. (j) Endogenous protein expression of ATRIP and interaction partners in EBV-LCLs from F1Pt, F1Fa, and HCs (n = 3). β-Tubulin was used as loading control. Western blot image is reflective of two independent experiments. (k) Quantification in arbitrary units of digitized chemiluminescent signals from Fig. 1 e normalized to β-tubulin signal from the same lane. Graph depicts fold change of normalized protein levels over the mean of HCs (n = 3) of at least four immunoblots. Source data are available for this figure: SourceDataFS1. Refer to the image caption for details.

Expanded genetic and molecular analysis confirms complete loss-of-function ATRIP variant in patient F1Pt . (a) Photographs of patients F1Pt and F46.1 demonstrating facial similarities, including sloping forehead and beak-like nose. (b) Weight (Wgt), height (Hgt), and head circumference (occipital frontal circumference; OFC) at birth plotted as z-scores (SD from population mean for age and sex). Dashed line at −2 SD indicates cut-off for normal population distribution. ATRIP patients are denoted by red dots; previous reported ATR patients are denoted by blue dots. (c) Electropherograms of genomic DNA extracted from blood for F1Pt and a HC. Nucleotide numbering is in accordance with ENST00000320211.1. Images represent results from five independent experiments. (d) Population genetics: Highest SpliceAI Delta Score against gnomAD v4.0.0. allele frequency (AF) for splice region variants in ATRIP (ENST00000320211.1). Splice region variants are defined as nucleotide changes within the ±20 base pairs (bp) flanking the exon. Black dots and blue cross signs represent heterozygous and homozygous variants, respectively. More details regarding homozygous splice variants can be found in Table S4. Red shaded dots represent ATRIP variants of interest (c.829+5G>T and c.829+2T>G). (e) Fragment analysis and size profiles of PCR-amplified cDNA extracted from fibroblasts for F1Pt and a HC. Arrows indicate the position of forward and reverse primers used for PCR amplification. Percentages represent relative quantification of the 538 bp wild type (WT) and 380 bp mutant (r.7671_829del) fragment. Data are reflective of two independent experiments. (f) Electropherograms of cDNA extracted from PHA blasts for F1Fa (father), F1Mo (mother), and a HC. Nucleotide numbering is in accordance with ENST00000320211.1. Data are reflective of five independent experiments. (g) Sashimi plot of targeted RNA-seq data generated in Integrative Genomics Viewer. Input RNA was extracted from PHA blasts of F1Pt and a HC. Exon numbering is in accordance with ENST00000320211.1. (h) Fragment analysis of PCR-amplified cDNA using two primer pairs (S1: E3–E5; S2: E5–E7, indicated by arrows) on fibroblasts from F1Pt and a HC. Data are reflective of two independent experiments. (i) Reverse transcription quantitative PCR (RT-qPCR) analysis on fibroblasts of F1Pt and HCs (n = 3) of amplicon in exon 3–4 and exon 5–6. The relative expression to β-actin in a logarithmic scale is shown. Data from two independent experiments are shown. (j) Endogenous protein expression of ATRIP and interaction partners in EBV-LCLs from F1Pt, F1Fa, and HCs (n = 3). β-Tubulin was used as loading control. Western blot image is reflective of two independent experiments. (k) Quantification in arbitrary units of digitized chemiluminescent signals from Fig. 1 e normalized to β-tubulin signal from the same lane. Graph depicts fold change of normalized protein levels over the mean of HCs (n = 3) of at least four immunoblots. Source data are available for this figure: SourceDataFS1.

This Feature Is Available To Subscribers Only

or Create an Account

Close Modal
Close Modal