<?xml version="1.0" encoding="us-ascii"?>
<!-- DFIN ActiveDisclosure(SM) XBRL Schema Document - http://www.dfinsolutions.com/ -->
<!-- Creation Date      : 2021-05-12T05:29:08.9254500+00:00 -->
<!-- Version            : 5.0.1.615 -->
<!-- Package ID         : 5a2a46614a554edd96a6cea73c9999df -->
<!-- Copyright (c) 2021 Donnelley Financial Solutions, Inc. All Rights Reserved. -->
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  <xsd:element id="atha_NetSalesExemptFromRoyaltyPayment" name="NetSalesExemptFromRoyaltyPayment" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="atha_RoyaltyObligation" name="RoyaltyObligation" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="credit" />
  <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_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_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_CommonStockWarrantsMember" name="CommonStockWarrantsMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="atha_SharesIssuableUponExerciseOfOutstandingCommonStockOptionsAndVestingOfOutstandingCommonRestrictedStockUnitsGrantedMember" name="SharesIssuableUponExerciseOfOutstandingCommonStockOptionsAndVestingOfOutstandingCommonRestrictedStockUnitsGrantedMember" 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_ShareBasedCompensationMaximumAnnualIncreaseInNumberOfSharesThatMayBeIssuedUnderPlan" name="ShareBasedCompensationMaximumAnnualIncreaseInNumberOfSharesThatMayBeIssuedUnderPlan" type="xbrli:sharesItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="atha_ShareBasedCompensationPercentageOfNumberSharesOfCommonStockIssuedAndOutstandingOnImmediateProceeding" name="ShareBasedCompensationPercentageOfNumberSharesOfCommonStockIssuedAndOutstandingOnImmediateProceeding" type="num:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="atha_TwoThousandAndTwentyEquityIncentivePlanMember" name="TwoThousandAndTwentyEquityIncentivePlanMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="atha_TowThousandAndTwentyEmployeeStockPurchasePlanMember" name="TowThousandAndTwentyEmployeeStockPurchasePlanMember" 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_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsAndRestrictedStockUnitGranted" name="ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsAndRestrictedStockUnitGranted" 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_ExercisePriceTenMember" name="ExercisePriceTenMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="atha_ExercisePriceElevenMember" name="ExercisePriceElevenMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="atha_ExercisePriceTwelveMember" name="ExercisePriceTwelveMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="atha_ExercisePriceThirteenMember" name="ExercisePriceThirteenMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="atha_ExercisePriceFourteenMember" name="ExercisePriceFourteenMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="atha_ExercisePriceFifteenMember" name="ExercisePriceFifteenMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="atha_ExercisePriceSixteenMember" name="ExercisePriceSixteenMember" 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_NonVestedRestrictedStockAwardsMember" name="NonVestedRestrictedStockAwardsMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="atha_NonVestedRestrictedStockUnitsMember" name="NonVestedRestrictedStockUnitsMember" 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:element id="atha_EmployeeStockPurchasePlanMember" name="EmployeeStockPurchasePlanMember" type="nonnum:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
</xsd:schema>
