MARRVEL: Search Result

Category	Exp. no. variants	Obs. no. variants	Contraint metrics
Synonymous	{{ gnomADGeneRes.syn.exp.toFixed(1) }}	{{ gnomADGeneRes.syn.obs }}	Z = {{ gnomADGeneRes.syn.z.toFixed(2) }}	o/e = {{ gnomADGeneRes.syn.oe.toFixed(2) }} ({{ gnomADGeneRes.syn.oeLower.toFixed(2) }} - {{ gnomADGeneRes.syn.oeUpper.toFixed(2) }})
Missense	{{ gnomADGeneRes.mis.exp.toFixed(1) }}	{{ gnomADGeneRes.mis.obs }}	Z = {{ gnomADGeneRes.mis.z.toFixed(2) }}	o/e = {{ gnomADGeneRes.mis.oe.toFixed(2) }} ({{ gnomADGeneRes.mis.oeLower.toFixed(2) }} - {{ gnomADGeneRes.mis.oeUpper.toFixed(2) }})
LoF	{{ gnomADGeneRes.lof.exp.toFixed(1) }}	{{ gnomADGeneRes.lof.obs }}	pLIThis metric estimates the probability that a gene falls into the class of LoF-haploinsufficient genes, where pLI > 0.9 means high likelihood of intolerance of haploinsufficiency. = {{ gnomADGeneRes.lof.pLI.toFixed(2) }}	o/eo/e (with 90% CI) = o/e = observed / expected. If the upper bound of the Loss-of-function o/e CI < 0.35, then there is a high likelihood of intolerance of loss-of-function/haploinsufficiency = {{ gnomADGeneRes.lof.oe.toFixed(2) }} ({{ gnomADGeneRes.lof.oeLower.toFixed(2) }} - {{ gnomADGeneRes.lof.oeUpper.toFixed(2) }})

No matches found

Control Population Gene Summary {{exacGeneRes.symbol}} (ExAC Gene Table)

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Open on the ExAC website

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{{head}} z = Z score, pLI = Probability of LoF intolerance
{{item}} Loss of function Copy number variation

No matches found

Population Allele Frequencies (ExAC database)

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Open on the ExAC website

Allele count	{{exacRes.ExACalleleCount}}
Allele number	{{exacRes.ExACalleleNum}}
Homozygous count	{{exacRes.ExAChomCount}}
Allele frequency	{{exacRes.ExACalleleFreq}}
Gene	{{symbol}}

No matches found

Geno2MP Total Heterozygote CountSOX4

Geno2MP Total Homozygote CountSOX4

Disease Population (Geno2MP database)SOX4

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Open on the Geno2MP website

Variant	rsID	HPO Profiles	# het	# hom
{{item.chr}}:{{item.pos}} {{item.ref}}>{{item.alt}}	{{item.varId == '.' ? 'NA' : item.varId}}	{{item.hpoCount}}	{{item.hetCount}}	{{item.homCount}}

No matches found

BenignClinVar

Likely benignClinVar

PathogenicClinVar

Likely pathogenicClinVar

Risk factorClinVar

Uncertain significanceClinVar

Conflicting interpretationsClinVar

Reported Alleles from ClinVarSOX4

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Open on the NCBI ClinVar website

Variation	Location	Condition(s)	Clinical Significance	Review Status

{{row.title}}{{ row.title }}	{{row.chr ? 'Chr' + row.chr + ':' : ''}}{{row.start}}{{row.start}}-{{row.stop}}	{{row.condition}}	{{row.significance.description}}	{{row.significance.reviewStatus}}
{{row.title}}{{ row.title }}	{{row.chr ? 'Chr' + row.chr + ':' : ''}}{{row.start}}{{row.start}}-{{row.stop}}	{{row.condition}}	{{row.significance.description}}	{{row.significance.reviewStatus}}

No ClinVar variants found for SOX4

Copy Number Variation in Control Population (DGV Database){{dgvRes.chr + ':' + dgvRes.pos}}SOX4

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Position	Size	Type	Subtype	Frequency	Gain	Loss	Sample Size	References	Genes
{{item.chr}} {{item.start}} {{item.end}}	{{item.end - item.start}}	{{item.varType}}	{{item.varSubType}}	{{(item.freq \|\| (item.observedgains + item.observedlosses) / item.sampleSize).toFixed(8)}}	{{item.observedgains}}	{{item.observedlosses}}	{{item.sampleSize}}	{{item.pubmedId}}	{{aGene}}

No matches found

Gene Function Table{{orthologSymbol}}

No matches found

Show only best DIOPTv6 score gene

	Homolog	DIOPT Score	Expression	Molecular function
Human	{{orthologSymbol}} {{orthologSymbol}}	NA	No data available {{item.organ}}	No term based on experiment {{item}} Show {{GO.length - 5}} more {{item}} Hide
Rat	{{row.geneSymbol}}	{{row.dioptScore}}/11	No data available {{item.name}} Show all ({{row.expression.length}}) {{item.name}} Show only high scores	No term based on experiment {{item}} Show {{GO.length - 5}} more {{item}} Hide
Mouse	{{row.geneSymbol}}	{{row.dioptScore}}/13	No data available No tissue expressed in wild-type {{item.description}} Show {{row.wtExp.length - 5}} more {{item.description}} Hide	No term based on experiment {{item}} Show {{GO.length - 5}} more {{item}} Hide
Zebrafish	{{row.geneSymbol}}	{{row.dioptScore}}/12	No available data No structure expressed in wild-type {{item.description}} Show {{row.expression.length - 5}} more {{item.description}} Hide	No term based on experiment {{item}} Show {{GO.length - 5}} more {{item}} Hide
Drosophila	{{row.geneSymbol}}	{{row.dioptScore}}/12	{{item.description}} No FlyAtlas organ/tissue expression data available.	No term based on experiment {{item}} Show {{GO.length - 5}} more {{item}} Hide
C Elegans	{{row.geneSymbol}}	{{row.dioptScore}}/12		No term based on experiment {{item}} Show {{GO.length - 5}} more {{item}} Hide
Budding Yeast	{{row.geneSymbol}}	{{row.dioptScore}}/11		No term based on experiment {{item}} Show {{GO.length - 5}} more {{item}} Hide
Fission Yeast	{{row.geneSymbol}}	{{row.dioptScore}}/8		No term based on experiment {{item}} Show {{GO.length - 5}} more {{item}} Hide

Organ	Expression Level
{{exp.organ}}	{{exp.class}}

No data available

FlyAtlas Organ/Tissue Expression, larval vs. adult

< 10

< 100

< 500

< 1000

>= 1000

	Adult	Larval
{{item.description}}	{{item.atLevel > 0 ? item.atLevel.toFixed(1) : 'NA'}}{{item.atClass == 0 ? 'NA' : ''}}	{{item.ltLevel > 0 ? item.ltLevel.toFixed(1) : 'NA'}}{{item.ltClass == 0 ? 'NA' : ''}}

Human Gene Protein DomainsDIOPT v6{{alignSymbol}}

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Open on the DIOPT website

Index	Domain name	Domain start	Domain stop	Domain description	Protein ID	External ID
{{row.index}}	{{row.domainName}}	{{row.domainStart}}	{{row.domainStop}}	{{row.domainDescription}}	{{row.proteinId}}	{{row.externalId}}

Multiple Protein AlignmentDIOPT v6{{alignSymbol}}

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Open on the DIOPT website

No alignment data available

{{row.species}}{{row.sIdx}} {{ch}}[{{row.endIdx}}] {{row.mark}}

Highlight from

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hsHomo sapiens (Human)

rnRattus norvegicus (Rat)

mmMus musculus (Mouse)

drDanio rerio (Zebrafish)

dmDrosophila melanogaster (Fly)

ceCaenorhabditis elegans (Worm)

scSaccharomyces cerevisiae (Yeast)

spSchizosaccharomyces pombe (Fission yeast)