Table legend for arvasample.tsv

aa_substitution: Amino acid substitution in standard notation (e.g., A123V indicates alanine at position 123 changed to valine)
stability_score_0hr: Protein stability percentage at 0 hours post-expression 
stability_score_24hr: Protein stability percentage at 24 hours post-expression
stability_score_48hr: Protein stability percentage at 48 hours post-expression 
Half-life (hr): Calculated protein half-life in hours, representing the time required for 50% of the protein to degrade

The columns listed below are from Supplementary Table S3 of Trinidad et al., 2023

ID: Common identifier for variant; either HGVSp or HGVSc, depending on the mutation.
HGVSc: Human Genome Variation Society coding variant, signifying nucleotide modifications.
HGVSg_GRCh37: Human Genome Variation Society genomic coordinates for GRCh37 (Genome Reference Consortium Human Build 37).
HGVSp: Human Genome Variation Society protein variant, signifying amino acid changes.
Finalized severity: Final verdict for variant severity, taking into account patient data and ClinVar annotations, as well as CDS and/or full-length activity assay results.
Patient count: Number of individuals in the patient data set who possessed the mutation.
Patient references: Details for reference publications associated with the variant and the patient data set.
ClinVar pathogenicity: ClinVar’s categorical annotation for variant pathogenicity (e.g. pathogenic, likely pathogenic, benign, not provided).
Consequence: ClinVar's descriptor for molecular consequence for variant (e.g. missense variant, splice region variant, frameshift variant).
Final assay severity: Overall assay severity, summarizing the results of the CDS and full-length assays.
CDS activity severity: Severity determined from the CDS activity assay. Severe mutations have <2% WT-ARSA activity, while moderate variants exhibit 2%–4% WT and mild mutations have 4%–13% WT activity. Any mutation with activity above 13% is considered benign.
Full-length activity severity: Severity determined from the full-length activity assay. Severe mutations have <2% WT-ARSA activity, while moderate variants exhibit 2%–4% WT and mild mutations have 4%–13% WT activity. Any mutation with activity above 13% is considered benign.
CDS percent WT activity: Percent WT-ARSA activity in CDS assay, averaged across three biological replicates.
Full-length percent WT activity: Percent WT-ARSA activity in full-length assay, averaged across three biological replicates.
SIFT scores: Continuous pathogenicity score predicted via SIFT model, ranging from 0 to 1, with 1 indicating a tolerated/benign mutation.
SIFT group: Categorical pathogenicity annotation predicted via SIFT model (e.g. deleterious, tolerated, tolerated low confidence).
PolyPhen scores: Continuous pathogenicity score predicted via PolyPhen model, ranging from 0 to 1, with 0 indicating a tolerated/benign mutation.
PolyPhen group: Categorical pathogenicity annotation predicted via PolyPhen model (e.g. benign, probably damaging).
All AF: Overall allele frequency across all populations listed in gnomAD.
African AF – Other AF: Columns showing variant allele frequencies in the denoted populations.
Inbreeding coefficient: Variant’s inbreeding coefficient from gnomAD.
AC: Allele count.
AF: Allele frequency calculated from ‘AC’ divided by ‘AN’.
AN: Total number of ARSA alleles sequenced in gnomAD.
AC African – AC female: Columns showing allele counts for various populations.
AN African – AN female: Columns showing the number of ARSA alleles sequenced in each population.
Hom African – Hom female: Columns listing the number of homozygotes in gnomAD for each population.
Hom raw: Raw unfiltered number of ARSA homozygotes
Hom: Total number of ARSA homozygotes present in gnomAD.
Comments: Relevant details about variants’ severity in the patient data set, along with notes from reference publications.
RS# (dbSNP): Reference SNP, as in dbSNP databse.