<?xml version="1.0" encoding="us-ascii"?>
<!-- DFIN ActiveDisclosure(SM) XBRL Schema Document - http://www.dfinsolutions.com/ -->
<!-- Creation Date      : 2020-11-12T07:32:55.5779198+00:00 -->
<!-- Version            : 5.0.1.513 -->
<!-- Package ID         : b6497586a8de4d2ab7df08be3de7be97 -->
<!-- Copyright (c) 2020 Donnelley Financial Solutions, Inc. All Rights Reserved. -->
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  <xsd:element id="atha_GrantLiabilityMaximumAmountPayableUnderAgreement" name="GrantLiabilityMaximumAmountPayableUnderAgreement" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="atha_EstimatedFairValueOfGrantLiability" name="EstimatedFairValueOfGrantLiability" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="atha_DebtInstrumentMaturityMonthAndYear" name="DebtInstrumentMaturityMonthAndYear" type="xbrli:gYearMonthItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="atha_UnsecuredConvertibleNotesMember" name="UnsecuredConvertibleNotesMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="atha_SeriesB1ConvertiblePreferredStockMember" name="SeriesB1ConvertiblePreferredStockMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="atha_PaycheckProtectionProgramCARESActMember" name="PaycheckProtectionProgramCARESActMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="atha_OperatingLeaseExpirationMonthAndYear" name="OperatingLeaseExpirationMonthAndYear" type="xbrli:gYearMonthItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="atha_LaboratoryAndOfficeFacilitiesMember" name="LaboratoryAndOfficeFacilitiesMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="atha_BothellWashingtonMember" name="BothellWashingtonMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="atha_UniversityOfWashingtonSeattleMember" name="UniversityOfWashingtonSeattleMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="atha_SeriesAConvertiblePreferredStockMember" name="SeriesAConvertiblePreferredStockMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="atha_SeriesA1ConvertiblePreferredStockMember" name="SeriesA1ConvertiblePreferredStockMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="atha_ClassOfWarrantOrRightExercised" name="ClassOfWarrantOrRightExercised" type="xbrli:sharesItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" />
  <xsd:element id="atha_ConvertiblePreferredStockConversionPrice" name="ConvertiblePreferredStockConversionPrice" type="num:perShareItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" />
  <xsd:element id="atha_ConvertiblePreferredStockConversionPricePercentage" name="ConvertiblePreferredStockConversionPricePercentage" type="num:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="atha_SeriesBConvertiblePreferredStockMember" name="SeriesBConvertiblePreferredStockMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="atha_ClassOfWarrantOrRightPurchasePriceOneMember" name="ClassOfWarrantOrRightPurchasePriceOneMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="atha_StockOptionsOutstandingMember" name="StockOptionsOutstandingMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="atha_SharesAvailableForFutureGrantUnderTwoThousandTwentyEquityIncentivePlanMember" name="SharesAvailableForFutureGrantUnderTwoThousandTwentyEquityIncentivePlanMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="atha_SharesAvailableForFutureGrantUnderEmployeeStockPurchasePlanMember" name="SharesAvailableForFutureGrantUnderEmployeeStockPurchasePlanMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="atha_EmployeesAndDirectorsMember" name="EmployeesAndDirectorsMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="atha_AdvisorsMember" name="AdvisorsMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="atha_NonEmployeesMember" name="NonEmployeesMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="atha_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsWeightedAverageGrantDateFairValueOfOptionsGranted" name="ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsWeightedAverageGrantDateFairValueOfOptionsGranted" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="atha_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsAvailableForGrantAuthorized" name="ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsAvailableForGrantAuthorized" type="xbrli:sharesItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="atha_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsAvailableForGrantGranted" name="ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsAvailableForGrantGranted" type="xbrli:sharesItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="atha_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsAvailableForGrantExercised" name="ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsAvailableForGrantExercised" type="xbrli:sharesItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="atha_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsAvailableForGrantForfeitedAndExpired" name="ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsAvailableForGrantForfeitedAndExpired" type="xbrli:sharesItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="atha_ShareBasedCompensationSharesAuthorizedUnderStockOptionPlansExercisePrice" name="ShareBasedCompensationSharesAuthorizedUnderStockOptionPlansExercisePrice" type="num:perShareItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="atha_ExercisePriceOneMember" name="ExercisePriceOneMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="atha_ExercisePriceTwoMember" name="ExercisePriceTwoMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="atha_ExercisePriceThreeMember" name="ExercisePriceThreeMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="atha_ExercisePriceFourMember" name="ExercisePriceFourMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="atha_ExercisePriceFiveMember" name="ExercisePriceFiveMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="atha_ExercisePriceSixMember" name="ExercisePriceSixMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="atha_ExercisePriceSevenMember" name="ExercisePriceSevenMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="atha_ExercisePriceEightMember" name="ExercisePriceEightMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="atha_ExercisePriceNineMember" name="ExercisePriceNineMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="atha_ShareBasedCompensationArrangementByShareBasedPaymentAwardSubjectToRepurchaseUponDiscontinuedService" name="ShareBasedCompensationArrangementByShareBasedPaymentAwardSubjectToRepurchaseUponDiscontinuedService" type="xbrli:sharesItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" />
  <xsd:element id="atha_ConvertiblePreferredStockOnConvertedBasisMember" name="ConvertiblePreferredStockOnConvertedBasisMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="atha_UnvestedRestrictedStockAwardsMember" name="UnvestedRestrictedStockAwardsMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="atha_StockOptionsToPurchaseCommonStockMember" name="StockOptionsToPurchaseCommonStockMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
</xsd:schema>
