1. ABOUT THE DATASET
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Title:	ACP4 Variants In Hypoplastic Amelogenesis Imperfecta supplementary data

Creator(s): Lu Liu [1], Cheuk W. Au [1], Ummey Hany [1], Alice L. Rigby [1], Anesha Chauhan [2], Catriona Brown [2], Jessie Sims [3], Gina Murillo [4], Marìa Gabriela Acosta de Carmargo [5], Chris F. Inglehearn [1], Christopher M. Watson [1,3], Alan J. Mighell [1], Claire E.L. Smith [1]

Organisation(s): 1. University of Leeds. 2. Birmingham Dental Hospital 3. Leeds Teaching Hospitals Trust 4. University of Costa Rica 5. Universidad de Carabobo.  

Rights-holder(s): Copyright 2026 University of Leeds

Publication Year: 2026

Description: This deposit contains supplementary data for the publication "ACP4 Variants In Hypoplastic Amelogenesis Imperfecta". This includes all of the input files and scripts used to generate the protein models for the wild-type ACP4 protein and the various substitutions resulting from the genetic variants identified in the study. It also contains the script and pipeline used to analyse the whole exome sequencing data, including alignment, variant calling and filtering.

Cite as: Lu Liu, Cheuk W. Au, Ummey Hany, Alice L. Rigby, Anesha Chauhan, Catriona Brown, Jessie Sims, Gina Murillo, Marìa Gabriela Acosta de Carmargo, Chris F. Inglehearn, Christopher M. Watson, Alan J. Mighell, Claire E.L. Smith (2026): ACP4 Variants In Hypoplastic Amelogenesis Imperfecta supplementary data. University of Leeds. [Dataset] https://doi.org/10.5518/1814

Related publication: Lu Liu, Cheuk W. Au, Ummey Hany, Alice L. Rigby, Anesha Chauhan, Catriona Brown, Jessie Sims, Gina Murillo, Marìa Gabriela Acosta de Carmargo, Chris F. Inglehearn, Christopher M. Watson, Alan J. Mighell, Claire E.L. Smith. ACP4 Variants In Hypoplastic Amelogenesis Imperfecta. Calcified Tissues International. 2026. In review.

Contact: Dr Claire E. L. Smith c.e.l.smith@leeds.ac.uk

2. TERMS OF USE
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Copyright 2026, University of Leeds. Unless otherwise stated, this dataset is licensed under a Creative Commons Attribution 4.0 International Licence: https://creativecommons.org/licenses/by/4.0/.

3. PROJECT AND FUNDING INFORMATION
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Title: Research-informed diagnostic testing and disease modelling to develop treatment options and improve patient outcomes in Amelogenesis Imperfecta

Dates: 1st May 2024- 1st April 2027

Funding organisation: Wellcome Trust (WT093113MA), Rosetrees Trust (PGS19-2/10111 and PGL23 100152) and a Leeds Doctoral Scholarship.

4. CONTENTS
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File listing

Folder: Figures - this folder contains better quality versions or alternative format version of the figures generated from AlphaFold3, Rosetta and pymol
Figure 4.png - this shows the positions of all published ACP4 pathogenic variants on the ACP4 homodimer as well as a selection of variants designated benign. The lower section shows a violin ploy of the relative stability of the mutant compared to the wild-type protein for all of the variants.
Figure 5.png - this shows the positions and local effects of the ACP4 variants identified in this study.
Movie.gif - this is an animation of the ACP4 homodimer generated using pymol, showing the positions of each of the residues references in Figure 4.
Movie.mpg - this is an animation of the ACP4 homodimer generated using pymol, showing the positions of each of the residues references in Figure 4.

Folder: Rosetta - this folder contains all of the scripts needed to generate the models that we obtained from Rosetta
ACP4_homodimer_Alphafold3.pdb - The original file from Alphafold3 of the ACP4 homodimer, based on Uniprot: Q9BZG2.
Annotated_Homodimer.pdb - .pdb file of the annotated ACP4 homodimer that was used to create Figure 4 & animation.
InterPro Analysis.tsv - Interpro output file of functional analysis from ACP4 sequence.
Mutants/column_stats.csv - output file that include the means and standard deviations of all ACP4 mutants.
Run_Rosetta_mutate_ACW - Script used to run Rosetta mutate.
Run_Rosetta_relax_ACW - Script used to run initial relax using Rosetta. 
WT_Alphafold3.pdb - Original file from Alphafold3 of the ACP4 monomer. 
WT_relaxed_0065.pdb - The input file for running Rosetta_mutate.
WT-WT/mutate-output.csv - 1000x REU values per mutation and the dREU mutate-output_all.csv, this file was used as the input for the script deltaG.py script to generate WT-WT violin plot.
Within Rosetta there are folders entitled Mutants and WT-WT, these each contain:
deltaG.py - Script used to generate the violin plot shown in Figure 4.
mutate-output_all.csv - file used as the input for the script. It contains dREU values of each mutation.
mutate-output.csv - 1000x REU values per mutant and the delta REU values.
column_stats.csv - contains the relative stability values calculated using Rosetta (this file is only available for the Mutants since the WT is what it is measured against). 

Folder: WES script - this folder contains only one file: 
WES script.docx - this is the script used to identify the ACP4 variants from whole exome sequencing fastq files for Families 1-3. It details alignment, variant calling and filtering. 

5. METHODS
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Please see the Methods section in the associated publication: Lu Liu, Cheuk W. Au, Ummey Hany, Alice L. Rigby, Anesha Chauhan, Catriona Brown, Jessie Sims, Gina Murillo, Marìa Gabriela Acosta de Carmargo, Chris F. Inglehearn, Christopher M. Watson, Alan J. Mighell, Claire E.L. Smith. ACP4 Variants In Hypoplastic Amelogenesis Imperfecta. Calcified Tissues International. 2026.