DOI: 10.5061/dryad.n02v6wxbb
title: Investigating the implications of the <em>MC4R</em> gene variants on health disparities related to caloric intake and body composition in African American women

description: This study aimed to assess the frequency distribution of Melanocortin 4
 Receptor (MC4R) gene variants and their relationship to caloric intake and
 body composition in African American women, to understand how these
 factors influence eating habits and body composition. Fifty adults aged
 18-70 from the Southeastern United States participated in this
 cross-sectional study. MC4R variants were identified using targeted
 sequencing on an Illumina platform, with genomic DNA (gDNA) isolated from
 buccal cells. Caloric intake was estimated using Nutritionist-Pro software
 based on responses to the modified Diet History Questionnaire II (DHQ II),
 and body composition was measured with the BOD POD instrument.
description: # Investigating the implications of the *MC4R* gene variants on health
 disparities related to caloric intake and body composition in African
 American women Dataset
 DOI: [10.5061/dryad.n02v6wxbb](https://doi.org/10.5061/dryad.n02v6wxbb) ##
 Description of the data and file structure This study aimed to assess the
 frequency distribution of Melanocortin 4 Receptor (*MC4R*) gene variants
 and their relationship to caloric intake and body composition in African
 American women, to understand how these factors influence eating habits
 and body composition. Fifty adults aged 18-70 from the Southeastern United
 States participated in this cross-sectional study. *MC4R* variants were
 identified using targeted sequencing on an Illumina platform, with genomic
 DNA (gDNA) isolated from buccal cells. Caloric intake was estimated using
 Nutritionist-Pro software based on responses to the modified Diet History
 Questionnaire II (DHQ II), and body composition was measured with the BOD
 POD instrument. ### Files and variables #### File:
 Raw_Data_1__Subjects_001_050_Rev_Dryad.xlsx **Description:** This dataset
 contains de-identified human-targeted next-generation sequencing data on
 variants of the melanocortin 4 receptor (MC4R) gene. Fifty adults aged
 18-70 from the Southeastern United States participated in this
 cross-sectional study. MC4R variants were identified using targeted
 sequencing on an Illumina platform, with genomic DNA (gDNA) isolated from
 buccal cells. #### File: Raw_Data_1__Subjects_001_050_Rev_Dryad.csv
 **Description:** This is the same data in .csv format. **Data Coding
 Definitions** * Null (Variant Not Detected):  Indicates that the genetic
 variant of interest was actively assessed and not detected in the
 subject’s genomic data using the specified analytical methods. This
 reflects a true negative finding, not missing information. * Not
 Applicable: Indicates that the subject does not carry the relevant gene or
 genomic region in which the variant would occur; therefore, assessment of
 the variant is biologically or analytically inapplicable for this
 individual. * Not Available (Data Unavailable): Indicates that information
 regarding the genetic variant could not be retrieved from the referenced
 databases or data sources at the time of analysis. This reflects missing
 or inaccessible data, not biological absence. ##### Variables *
 Subject: Three-digit participant code * Priority: predicted MC4R variant
 of clinical/biological significance * Quality: base quality scores and
 variant caller confidence metrics * Location: mutation location of the
 variant within the MC4R gene * Mut_type: Single Nucleotide Polymorphism *
 Chr: Chromosome in which the variant is located * Start: start position of
 the mutation * End: end position of the mutation * Ref: base type of the
 reference genome * Alt: base type mutation * Vcf_mut: mutation following
 the Variant Call Format (VCF) allele notation * GT: genotype * AD: Allelic
 Depth * DP: Read Depth * GQ: Genotype quality value * FRE: mutation
 frequency * Func.refGene: functional classification of the variant *
 Gene.refGene: gene symbol * GeneDetail.refGene: gene-level annotation
 where the mutation is located * ExonicFunc.refGene: mutation function type
 at the protein code level * AAChange.refGene: amino acid changes resulting
 from the variant * Func.HGVS: variant description according to HGVS rule *
 AAChange.HGVS: amino acid changes according to HGVS rule *
 cytoBand: Cytogenetic band location of the variant on the chromosome *
 InterVar: Clinical interpretation of the variant using the InterVar tool *
 ACMG: ACMG/AMP evidence codes assigned to the variant * wgRna: Annotation
 indicating if the variant overlaps a known RNA element *
 genomicSuperDups: indicate if the variant falls within a repeat segment *
 rmsk: identify repetitive DNA elements overlapping the variant *
 gwasCatalog: Shows whether the variant was reported in prior GWAS studies
 * avsnp150: dbSNP identifier (build 150) assigned to the variant *
 1000g2015aug_all: Allele frequency of the variant in the total population
 from the 1000 Genomes Project (August 2015 release) *
 1000g2015aug_eas: Allele frequency of the variant in the East Asian
 population from the 1000 Genomes Project (August 2015 release) *
 esp6500siv2_all: Allele frequency of the variant in the NHLBI Exome
 Sequencing Project (ESP6500, SI-V2) * ExAC_ALL: Alternate allele frequency
 of the variant in the Exome Aggregation Consortium (ExAC) database across
 all populations * ExAC_EAS: Alternate allele frequency of the variant in
 the East Asian population within the ExAC database *
 gnomAD_exome_AF_raw: Raw alternate allele frequency of the variant in the
 Genome Aggregation Database (gnomAD) exome dataset across all populations
 * gnomAD_exome_AF_eas: Alternate allele frequency of the variant in the
 East Asian population within the gnomAD exome dataset *
 gnomAD_genome_AF_raw: Raw alternate allele frequency of the variant in the
 gnomAD whole-genome dataset across all populations *
 gnomAD_genome_AF_eas: Alternate allele frequency of the variant in the
 East Asian population within the gnomAD whole-genome dataset *
 ICGC_Id: Identifier assigned to the variant in the ICGC database *
 ICGC_Occurrence: Reported occurrence of the variant across cancer studies
 within the ICGC database * iGeneTechDB: Annotation indicating whether the
 variant is recorded in the iGeneTech database * CLNALLELEID: ClinVar
 allele identifier corresponding to the variant * CLNDN: ClinVar disease
 name(s) associated with the variant * CLNDISDB: ClinVar disease annotation
 database * CLNREVSTAT: ClinVar review status for the variant *
 CLNSIG: ClinVar clinical significance of the variant * cosmic95: Presence
 of the variant in COSMIC database * HGMD: presence of the variant in the
 Human Gene Mutation Database * dbscSNV_ADA_SCORE: predicting the influence
 of the variant on alternative splicing using AdaBoost algorithm *
 dbscSNV_RF_SCORE: predicting the influence of the variant on alternative
 splicing using Random Forest algorithm * SIFT_score: indicates the effect
 of the mutation on the protein * SIFT_pred: prediction indicating the
 mutation affects multiple proteins * SIFT4G_score: Another version of SIFT
 score * SIFT4G_pred: Another version of SIFT pred *
 Polyphen2_HDIV_score: PolyPhen2 predicts the score of the impact of the
 mutation on the protein sequence * Polyphen2_HDIV_pred: The prediction
 results of the Polyphen2 based on HDIV database *
 Polyphen2_HVAR_score: PolyPhen2 predicts the score of the impact of the
 mutation on the protein sequence based on the HumanVar database *
 Polyphen2_HVAR_pred: The prediction results of the Polyphen2 based on HVAR
 database * LRT_score: The prediction score of LRT software * LRT_pred: The
 prediction result of LRT software * MutationTaster_score: The prediction
 score of MutationTaster software * MutationTaster_pred: The prediction
 result of MutationTaster software * MutationAssessor_score: The prediction
 score of MutationAssessor software * MutationAssessor_pred: The prediction
 result of MutationAssessor software * FATHMM_score: The prediction score
 of FATHMM software * FATHMM_pred: The prediction result of FATHMM software
 * PROVEAN_score: The prediction score of the PROVEAN * PROVEAN_pred: The
 prediction results of the PROVEAN * VEST4_score: The score of variant
 effect scoring tool * MetaSVM_score: prediction scores of SIFT, PolyPhen
 and MutationAssessor to predict the harmfulness of mutations *
 MetaSVM_pred: prediction scores of SIFT, PolyPhen and MutationAssessor to
 predict the harmfulness of mutations * ClinPred_score: predicts the
 harmfulness of non-synonymous mutations * ClinPred_pred: the prediction
 result of ClinPred * CADD_raw: score the harmfulness of SNV and InDel *
 CADD_phred: PHRED-scaled CADD score * fathmm-MKL_coding_score: Functional
 annotation for coding variants using the FATHMM-MKL algorithm *
 fathmm-MKL_coding_pred: Functional annotation for coding variants using
 the FATHMM-MKL algorithm * GERP++_NR: measures evolutionary constraint *
 GERP++_RS: Rejected substitution score from GERP++; measures evolutionary
 constraint * OMIM_Inheritance: Annotation to the Human Mendelian
 Inheritance Disease Database * OMIM_Disease: Disease name from OMIM
 associated with the variant * HGMD_Disease: Disease name(s) from HGMD
 associated with the variant * GO: Gene Ontology terms associated with the
 gene containing the variant * KEGG_pathway: KEGG_pathway annotation
 results ## Code/software Microsoft Excel ## Access information Other
 publicly accessible locations of the data: * n/a Data was derived from the
 following sources: * n/a ## Human subjects data Participants signed an
 informed consent form, and each received a unique code. All direct and
 indirect identifiers were removed or generalized to prevent
 re-identification.