Gene list
Column names Description
EntrezID Entrez Gene ID.
Symbol Gene Name. RefSeq gene definition is used.
Chr Chromosome number.
Band CytoBand location.
Type
Gene Information Gene Information link in PsyMuKB.
Mutation Information Mutation Information link in PsyMuKB.
 Gene detail
Column names Description
Basic information EntrezID Entrez Gene ID.
Official symbol Gene symbol.
Synonyms Alternative names of the gene.
Description Gene description.
Location CytoBand location.
Type of protein Protein type.
External annotation External annotation from Genecard.
Summary uniprot_summary Uniprot gene summary.
refseq_summary Refseq gene summary.
Assessment table PLI The probability of being loss-of-function (LoF) intolerant. See the Comment column information of table for details.
Haploinsufficiency (HI) score rank Predicted probability of exhibiting haploinsufficiency. See the Comment column information of table for details.
Gene brain expressed Queried gene is expressed in brain tissues. See the Comment column information of table for details.
Protein brain expressed Queried protein is expressed in brain tissues. See the Comment column information of table for details.
Carrying LoF DNMs Number of loss-of-function DNMs hit the queried gene. See the Comment column information of table for details.
Carrying missense DNMs Number of missense DNMs hit the queried gene. See the Comment column information of table for details.
FMRP binding targets FMRP inteacting parters. See the Comment column information of table for details.
Postsynaptic density (PSD) Protein associates with postsynaptic membranes of excitatory synapses. See the Comment column information of table for details.
Human essential genes Genes are thought to be critical for human survival. See the Comment column information of table for details.
Variants Table Variant type Indicates the type of variant.
Phenotypes Observable clinical symptoms of the patient.
Gencode/Refseq transcripts TranscriptID Ensembl identifiers for transcripts.
Transcript_exon_region Exon regions the transcript hits.
Coding_exon_region Coding exon regions the transcript hits.
Enhancer Chrom Chromosome number.
Start The start position of the enhancer on the chromosome.
End The end position of the enhancer on the chromosome.
Score Gene-GeneHancer associations and likelihood-based scores were generated using information that helps link regulatory elements to genes.
Attributes A list of all genes associated with the GeneHancer.
Target_GeneID Gene entrez ID of enhancer's target.
Promoter Chrom Chromosome number.
Start The start position of the promoter on the chromosome.
End The end position of the promoter on the chromosome.
Protein-Protein Interactions Table Symbol A Gene symbol of Protein-Protein Interaction participant geneA.
GeneA Coding DNM Count Coding DNM counts of GeneA.
Symbol B Gene symbol of Protein-Protein Interaction participant geneB.
GeneB Coding DNM Count Coding DNM counts of GeneB..
Interaction Detection Method Detection method of the Protein-Protein Interaction.
Publication Publications indicate the Protein-Protein Interaction.
Evidence Evidence counts of the Protein-Protein Interaction.
 Mutation list
Column names Description
Coding de novo mutations Chr Chromosome number.
Position Genomic position on the chromosome as to hg19 (1-based coordinate).
Variant Reference nucleotide allele > Alternate nucleotide allele.
Exonic Func Exonic variant function, e.g., nonsynonymous, synonymous, frameshift insertion.
Case or control Sample from case or control set.
Primary Phenotype Main phenotype of the patients for inclusion in the study.
Potential Severity Level Impact level evaluated by types of mutations and predict tools (SIFT, Polyphen2, GERP++, CADD, and Clinvar).
LoF Loss of function.
SIFT SIFT prediction. .
Polyphen2 Pholyphen2 prediction based on HDIV.
GERP++ GREP++ "rejected substitutions" (RS) score.
CADD Combined Annotation Dependent Depletion, phred-scaled scores, 10 means 10% percentile highest scores, 20 means 1% percentile highest scores, and 30% means 0.1% percentile highest scores.
ClinVar ClinVar_SIG.
Mutation site in protein structure Mutation site in protein structure.
Sample ID Sample ID of the variant carrier.
Study The Study that indicates the variant.
Validation Validation status of the variant.
1000G_ALL Average alternative allele frequency of the variant in all 1000G sets.
ExAC_Freq Frequency of the variant in the ExAC database.
gnomAD_exome_ALL Allele frequency in gnomAD exome set.
gnomAD_genome_ALL Allele frequency in gnomAD genome set.
DeepSea_Score DeepSEA score from DeepSEA, a deep learning-based algorithmic framework for predicting the chromatin effects of sequence alterations with single nucleotide sensitivity.
Non-coding de novo mutations Chr Chromosome number.
Position Genomic position on the chromosome as to hg19 (1-based coordinate).
Variant Reference nucleotide allele > Alternate nucleotide allele.
Func.refGene Regions (e.g., exonic, intronic, non-coding RNA)) that one variant hits; .
Potential Severity Level Impact level evaluated by types of mutations and predict tools (SIFT, Polyphen2, GERP++, CADD, and Clinvar).
Case or control Sample from case or control set.
Primary Phenotype Main phenotype of the patients for inclusion in the study.
Sample ID Sample ID of the variant carrier.
Study The Study that indicates the variant.
Validation Validation status of the variant.
1000G_ALL Average alternative allele frequency of the variant in all 1000G sets.
CADD_phred Combined Annotation Dependent Depletion, phred-scaled scores, 10 means 10% percentile highest scores, 20 means 1% percentile highest scores, and 30% means 0.1% percentile highest scores.
GnomAD_genome_ALL Allele frequency in gnomAD genome set.
Enhancer_ID The identifier of enhancer.
Enhancer_Chr The chromosome number of the enhancer.
Enhancer_Start The start position of the enhancer on the chromosome.
Enhancer_End The end position of the enhancer on the chromosome.
Enhancer_Target_GeneID The target gene ID of the enhancer.
Promoter_ID The identifier of promoter.
Promoter_Chr The chromosome number of the promoter.
Promoter_Start The start position of the promoter on the chromosome.
Promoter_End The end position of the promoter on the chromosome.
Promoter_Target_Geneid The target gene ID of the promoter.
Promoter_Gene_Symbol The target gene symbol of the promoter.
DeepSea_Score DeepSEA score from DeepSEA, a deep learning-based algorithmic framework for predicting the chromatin effects of sequence alterations with single nucleotide sensitivity.
De novo copy number variations Chr Chromosome number.
CNV_ID CNV ID.
Band CytoBand location of the CNV.
Mutation Type Mutation type of the CNV.
Start CNV start position in hg19.
End CNV end position in hg19.
Disorder Clinical phenotype of the CNV carrier.
Patient ID Patient ID of the CNV carrier.
Study The Study that indicates the CNV.
Of probands The total number of probands involved in the study.
Of controls The total number of controls involved in the study.
Gene Symbols Genes the CNV hits.
 Mutation detail
Column names Description
Coding de novo mutations Chr Chromosome number.
Position Genomic position on the chromosome as to hg19 (1-based coordinate).
Variant Reference nucleotide allele > Alternate nucleotide allele.
Gene Gene symbol. RefSeq gene definition is used.
Case or control Sample from case or control set.
Func.refGene Regions (e.g., exonic, intronic, non-coding RNA)) that one variant hits; .
ExonicFunc.refGene Exonic variant function (non-synonymous, synonymous, etc).
SampleID Sample ID of the variant carrier.
Study The Study that indicates the variant.
NumProbands The total number of probands involved in the study.
NumControls The total number of controls involved in the study.
SequenceType The used sequencing technology.
PrimaryPhenotype Main phenotype of the patients for inclusion in the study.
Validation Validation status of the variant.
Sex Gender of the variant carrier.
Source The source used to collect the mutation.
AAChange.refGene Amino acid changes refers to hg19 reference sequence.
1000G_ALL Average alternative allele frequency of the variant in all 1000G sets.
1000G_EAS Alternative allele frequency of the variant in 1000G East Asian sets.
Mutation site in protein structure Mutation site in protein structure.
ExAC_Freq Frequency of the variant in the ExAC database.
ExAC_EAS Frequency of the variant in the ExAC East Asian set.
ESP6500si_ALL Allele frequency in ESP6500si dataset.
dbSNP rsID of the variant.
ClinVar_SIG Variant Clinical Significance , including unknown, untested, non-pathogenic, probable-non-pathogenic, probable-pathogenic, pathogenic, drug-response,histocompatibility, other.
SIFT_pred SIFT prediction.
Polyphen2_HVAR_pred Polyphen2 prediction based on HVAR.
LRT_pred LRT prediction.
FATHMM_pred FATHMM prediction.
CADD_phred Combined Annotation Dependent Depletion, phred-scaled scores, 10 means 10% percentile highest scores, 20 means 1% percentile highest scores, and 30% means 0.1% percentile highest scores.
Eigen_coding_or_noncoding Aggregate functional score for variants estimated by Eigen.
GERP++_RS GREP++ "rejected substitutions" (RS) score.
gnomAD_exome_ALL Allele frequency in gnomAD exome set.
gnomAD_exome_EAS Allele frequency in gnomAD exome East Asian set.
gnomAD_genome_ALL Allele frequency in gnomAD genome set.
gnomAD_genome_EAS Allele frequency in gnomAD genome East Asian set.
Enhancer Id The identifier of enhancer.
Enhancer Chr The chromosome number of the enhancer.
Enhancer Start The start position of the enhancer on the chromosome.
Enhancer End The end position of the enhancer on the chromosome.
Enhancer target gene id The target gene ID of the enhancer.
DeepSea_Score DeepSEA score from DeepSEA, a deep learning-based algorithmic framework for predicting the chromatin effects of sequence alterations with single nucleotide sensitivity.
Haploinsufficiency_Score Predicted probability of exhibiting haploinsufficiency.
Haploinsufficiency_Rank High ranks (e.g. 0-10%) indicate a gene is more likely to exhibit haploinsufficiency, low ranks (e.g. 90-100%) indicate a gene is more likely to NOT exhibit haploinsufficiency.
Non-coding de novo mutations Chr Chromosome number.
Position Genomic position on the chromosome as to hg19 (1-based coordinate).
Variant Reference nucleotide allele > Alternate nucleotide allele.
Gene Gene symbol. RefSeq gene definition is used.
Case or control Sample from case or control set.
Func.refGene Regions (e.g., exonic, intronic, non-coding RNA)) that one variant hits;.
ExonicFunc.refGene Exonic variant function, e.g., nonsynonymous, synonymous, frameshift insertion.
SampleID Sample ID of the variant carrier.
Study The Study that indicates the variant.
NumProbands The total number of probands involved in the study.
NumControls The total number of controls involved in the study.
SequenceType The used sequencing technology.
PrimaryPhenotype Main phenotype of the patients for inclusion in the study.
Validation Validation status of the variant.
Sex Gender of the variant carrier.
Source The source used to collect the mutation.
AAChange.refGene Amino acid changes refers to hg19 reference sequence.
1000G_ALL Average alternative allele frequency of the variant in all 1000G sets.
dbSNP rs number from dbSNP build.
ClinVar_SIG Variant Clinical Significance , including unknown, untested, non-pathogenic, probable-non-pathogenic, probable-pathogenic, pathogenic, drug-response,histocompatibility, other.
LRT_pred LRT prediction, D(eleterious), N(eutral) or U(nknown).
FATHMM_pred FATHMM prediction, D(damaging) or T(tolerated).
CADD_phred Combined Annotation Dependent Depletion, phred-scaled scores, 10 means 10% percentile highest scores, 20 means 1% percentile highest scores, and 30% means 0.1% percentile highest scores.
Eigen_coding_or_noncoding Coding or non-coding .
GERP++_RS GERP++ RS score, the larger the score, the more conserved the site is.
gnomAD_genome_ALL Allele frequency in gnomAD genome set.
gnomAD_genome_EAS Allele frequency in gnomAD genome East Asian set.
gnomAD_genome_ALL Allele frequency in gnomAD genome set.
enh_id The identifier of enhancer.
enh_chr The chromosome number of the enhancer.
enh_start The start position of the enhancer on the chromosome.
enh_end The end position of the enhancer on the chromosome.
enh_target_geneid The target gene ID of the enhancer.
pro_id The identifier of promoter.
pro_chr The chromosome number of the promoter.
pro_start The start position of the promoter on the chromosome.
pro_end The end position of the promoter on the chromosome.
pro_target_geneid The target gene ID of the promoter.
pro_gene_symbol The target gene symbol of the promoter.
DeepSea_Score DeepSEA score from DeepSEA, a deep learning-based algorithmic framework for predicting the chromatin effects of sequence alterations with single nucleotide sensitivity.
Haploinsufficiency_Score Predicted probability of exhibiting haploinsufficiency.
Haploinsufficiency_Rank High ranks (e.g. 0-10%) indicate a gene is more likely to exhibit haploinsufficiency, low ranks (e.g. 90-100%) indicate a gene is more likely to NOT exhibit haploinsufficiency.
Impacted isoform list Isoform ID The ID of the isoform.
Transcript ID The transcript ID of the isoform.
protein sequence ID The protein ID of the isoform.
gene ID The gene ID of the isoform.
Note Whether this isoform was assembled in reference hg19.

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