ClinVar Miner

List of variants reported as likely benign for amino acid metabolism disease by Illumina Laboratory Services, Illumina

Included ClinVar conditions (117):
Minimum submission review status: Collection method:
Minimum conflict level:
ClinVar version:
Total variants: 259
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_006623.3(PHGDH):c.*200A>G rs17258425 0.11740
NM_005589.4(ALDH6A1):c.*433C>T rs1135886 0.11114
NM_000709.3(BCKDHA):c.-34T>G rs45500792 0.09943
NM_000709.4(BCKDHA):c.116C>A (p.Pro39His) rs11549936 0.07892
NM_000156.6(GAMT):c.*276C>T rs266810 0.07427
NM_000156.6(GAMT):c.*151T>C rs659460 0.07383
NM_000156.6(GAMT):c.*311C>G rs266811 0.06572
NM_004577.3(PSPH):c.-632C>T rs34822782 0.03837
NM_003748.4(ALDH4A1):c.-4C>A rs9426797 0.03554
NM_000277.3(PAH):c.707-7A>T rs62508624 0.02868
NM_000277.2(PAH):c.-147C>T rs62517177 0.02849
NM_005518.4(HMGCS2):c.*332A>C rs56828380 0.02618
NM_000360.4(TH):c.1401C>T (p.Asp467=) rs3842724 0.02616
NM_058179.4(PSAT1):c.*592A>C rs115361057 0.02603
NM_003748.4(ALDH4A1):c.47C>T (p.Pro16Leu) rs146450609 0.02500
NM_001918.5(DBT):c.*8983dup rs67820832 0.02408
NM_000170.3(GLDC):c.-186del rs140030144 0.02402
NM_000170.3(GLDC):c.671G>A (p.Arg224His) rs28617412 0.02214
NM_003748.4(ALDH4A1):c.*35C>T rs2230710 0.02193
NM_000137.4(FAH):c.1021C>T (p.Arg341Trp) rs11555096 0.02131
NM_003748.4(ALDH4A1):c.-7A>G rs9426679 0.02115
NM_000156.6(GAMT):c.*11C>T rs149268921 0.01866
NM_000071.3(CBS):c.*383C>T rs73372352 0.01854
NM_000170.2(GLDC):c.*557C>G rs73639311 0.01818
NM_003748.4(ALDH4A1):c.744C>T (p.Ile248=) rs60427141 0.01815
NM_003748.4(ALDH4A1):c.603+14G>A rs79637190 0.01743
NM_005589.4(ALDH6A1):c.349-13G>A rs45510700 0.01704
NM_000187.4(HGD):c.1221G>A (p.Ala407=) rs146206905 0.01639
NM_000277.3(PAH):c.963C>T (p.Leu321=) rs61747292 0.01582
NM_000161.3(GCH1):c.*1463_*1464dup rs55885280 0.01521
NM_005589.4(ALDH6A1):c.636G>A (p.Glu212=) rs8008790 0.01439
NM_003748.4(ALDH4A1):c.1631C>T (p.Pro544Leu) rs72953172 0.01344
NM_000207.3(INS):c.36G>A (p.Ala12=) rs3842744 0.01335
NM_003748.4(ALDH4A1):c.1162T>C (p.Phe388Leu) rs41273175 0.01334
NM_001918.5(DBT):c.*8607G>A rs150241889 0.01296
NM_000360.4(TH):c.1278G>A (p.Thr426=) rs36097848 0.01234
NM_000687.4(AHCY):c.112C>T (p.Arg38Trp) rs13043752 0.01213
NM_001352514.2(HLCS):c.*1744G>A rs117270429 0.01206
NM_003748.4(ALDH4A1):c.*903C>T rs148846466 0.01203
NM_000071.3(CBS):c.304A>C (p.Lys102Gln) rs34040148 0.01138
NM_005518.4(HMGCS2):c.*165C>T rs138575225 0.01059
NM_000187.4(HGD):c.142G>T (p.Ala48Ser) rs138846036 0.01021
NM_003748.4(ALDH4A1):c.584C>T (p.Thr195Met) rs72936434 0.00992
NM_001080.3(ALDH5A1):c.*784C>T rs115442722 0.00977
NM_000170.3(GLDC):c.*257G>A rs111326356 0.00972
NM_003748.4(ALDH4A1):c.433G>A (p.Ala145Thr) rs113846237 0.00952
NM_000207.3(INS):c.-9C>T rs5505 0.00878
NM_001918.5(DBT):c.*8552A>T rs543411196 0.00862
NM_000353.3(TAT):c.*813G>C rs182924845 0.00777
NM_001352514.2(HLCS):c.*2624G>A rs73210780 0.00769
NM_015702.3(MMADHC):c.87A>C (p.Lys29Asn) rs61750442 0.00751
NM_000481.4(AMT):c.631G>A (p.Glu211Lys) rs116192290 0.00735
NM_001080.3(ALDH5A1):c.*1239T>G rs191960134 0.00705
NM_020686.6(ABAT):c.*1202G>A rs75730008 0.00704
NM_001080.3(ALDH5A1):c.*1877A>G rs41271787 0.00686
NM_000170.3(GLDC):c.52G>T (p.Gly18Cys) rs535143891 0.00670
NM_000170.3(GLDC):c.2203G>T (p.Val735Leu) rs143119940 0.00650
NM_000071.3(CBS):c.1145+7C>T rs201158177 0.00620
NM_015702.3(MMADHC):c.473G>A (p.Arg158Gln) rs114276563 0.00611
NM_004577.4(PSPH):c.-442A>G rs184427284 0.00526
NM_001352514.2(HLCS):c.331-7157C>T rs149104163 0.00524
NM_000137.4(FAH):c.315-14G>A rs139830755 0.00521
NM_005589.4(ALDH6A1):c.*1904G>C rs147392789 0.00503
NM_002860.4(ALDH18A1):c.2207-3C>T rs149309642 0.00472
NM_000170.3(GLDC):c.1707+8G>A rs144666843 0.00464
NM_020686.6(ABAT):c.*1075C>T rs117516993 0.00462
NM_000108.5(DLD):c.543A>T (p.Ile181=) rs61749952 0.00461
NM_000317.3(PTS):c.315-3T>C rs189365250 0.00436
NM_000170.3(GLDC):c.1705G>A (p.Ala569Thr) rs151268759 0.00419
NM_004577.4(PSPH):c.-456T>C rs190216482 0.00411
NM_000687.4(AHCY):c.28+7C>T rs201479827 0.00410
NM_000687.4(AHCY):c.367G>A (p.Gly123Arg) rs41301825 0.00406
NM_012463.4(ATP6V0A2):c.*998T>C rs12298446 0.00401
NM_001352514.2(HLCS):c.*1725A>G rs73398120 0.00399
NM_001352514.2(HLCS):c.*3247A>G rs114061673 0.00386
NM_000048.4(ASL):c.*218C>T rs115226772 0.00375
NM_006623.4(PHGDH):c.*151C>G rs112584109 0.00373
NM_000709.4(BCKDHA):c.975C>T (p.Leu325=) rs55940366 0.00365
NM_000156.6(GAMT):c.*89C>A rs558767159 0.00362
NM_005589.4(ALDH6A1):c.414A>G (p.Val138=) rs4899491 0.00354
NM_001352514.2(HLCS):c.1002C>T (p.Ala334=) rs116114362 0.00352
NM_001080.3(ALDH5A1):c.961G>A (p.Val321Met) rs115784602 0.00349
NM_000170.3(GLDC):c.678C>T (p.His226=) rs12006003 0.00338
NM_002860.4(ALDH18A1):c.*292C>T rs78053774 0.00329
NM_001080.3(ALDH5A1):c.*1883C>T rs139473699 0.00318
NM_001352514.2(HLCS):c.2113G>A (p.Glu705Lys) rs149736764 0.00315
NM_012463.4(ATP6V0A2):c.-117C>T rs532360215 0.00315
NM_000481.4(AMT):c.1145G>A (p.Arg382Gln) rs141246107 0.00299
NM_015702.3(MMADHC):c.-8C>T rs180812156 0.00282
NM_006721.4(ADK):c.*740C>T rs150465356 0.00276
NM_012463.4(ATP6V0A2):c.*785T>C rs146660715 0.00262
NM_000170.3(GLDC):c.1331G>A (p.Cys444Tyr) rs142099123 0.00261
NM_001352514.2(HLCS):c.*19C>T rs137949852 0.00259
NM_012463.4(ATP6V0A2):c.1258G>T (p.Val420Leu) rs138716143 0.00258
NM_001080.3(ALDH5A1):c.130C>G (p.Leu44Val) rs185042766 0.00257
NM_058179.4(PSAT1):c.*865C>G rs529821810 0.00257
NM_006721.4(ADK):c.66-24106T>C rs192064997 0.00255
NM_183050.4(BCKDHB):c.*1798C>T rs535334878 0.00251
NM_004577.4(PSPH):c.72G>C (p.Thr24=) rs145408555 0.00245
NM_000108.5(DLD):c.507C>T (p.Gly169=) rs144351432 0.00241
NM_000137.4(FAH):c.1259G>A (p.Ter420=) rs61747586 0.00241
NM_000048.4(ASL):c.162C>T (p.Leu54=) rs140221164 0.00238
NM_000170.3(GLDC):c.1229G>A (p.Arg410Lys) rs144090917 0.00234
NM_001080.3(ALDH5A1):c.1348G>A (p.Asp450Asn) rs144177566 0.00229
NM_005589.4(ALDH6A1):c.*1820G>A rs111624130 0.00225
NM_020686.6(ABAT):c.641T>C (p.Met214Thr) rs149271402 0.00219
NM_001080.3(ALDH5A1):c.480C>T (p.Ser160=) rs143486700 0.00217
NM_000071.3(CBS):c.*34G>A rs374464201 0.00214
NM_058179.4(PSAT1):c.367A>G (p.Ile123Val) rs116577685 0.00213
NM_000687.4(AHCY):c.744C>T (p.Asn248=) rs150175934 0.00210
NM_000108.5(DLD):c.*1640A>G rs148148357 0.00209
NM_006721.4(ADK):c.*375A>G rs185021662 0.00206
NM_000170.3(GLDC):c.2748G>A (p.Leu916=) rs139982267 0.00203
NM_000170.3(GLDC):c.2683A>G (p.Met895Val) rs141152043 0.00200
NM_020686.6(ABAT):c.30G>A (p.Leu10=) rs34813662 0.00200
NM_001918.5(DBT):c.1418A>G (p.Asn473Ser) rs75525811 0.00196
NM_001171993.2(HPD):c.-115+52A>G rs199549271 0.00192
NM_000071.3(CBS):c.954+8G>A rs76292057 0.00188
NM_000071.2(CBS):c.-160C>T rs112271970 0.00185
NM_000170.3(GLDC):c.1927-9A>G rs41281773 0.00180
NM_000187.4(HGD):c.129G>A (p.Gln43=) rs142789485 0.00165
NM_000481.4(AMT):c.*130G>T rs143731179 0.00149
NM_000156.6(GAMT):c.392-7C>T rs192416474 0.00144
NM_004577.4(PSPH):c.146G>A (p.Arg49Gln) rs144281276 0.00138
NM_000071.3(CBS):c.1359-14C>T rs115185587 0.00137
NM_000170.3(GLDC):c.*229C>G rs184498089 0.00135
NM_000709.4(BCKDHA):c.*334C>T rs528816040 0.00133
NM_001080.3(ALDH5A1):c.*40T>C rs146793715 0.00132
NM_000187.4(HGD):c.919C>T (p.Arg307Cys) rs143556739 0.00124
NM_001080.3(ALDH5A1):c.*3190A>G rs182106500 0.00117
NM_000481.4(AMT):c.*416C>T rs571207015 0.00114
NM_006721.4(ADK):c.1088G>A (p.Ter363=) rs148819558 0.00108
NM_000071.3(CBS):c.1643G>A (p.Arg548Gln) rs150828989 0.00105
NM_000709.4(BCKDHA):c.15C>T (p.Ile5=) rs17173144 0.00103
NM_000170.3(GLDC):c.*236G>T rs537707294 0.00102
NM_000360.4(TH):c.-7C>T rs199925956 0.00098
NM_032316.3(NICN1):c.*2307G>C rs544461335 0.00097
NM_001080.3(ALDH5A1):c.13A>G (p.Ile5Val) rs200398000 0.00096
NM_000277.3(PAH):c.158G>A (p.Arg53His) rs118092776 0.00091
NM_000071.3(CBS):c.52C>T (p.Arg18Cys) rs201827340 0.00086
NM_001080.3(ALDH5A1):c.293C>G (p.Ala98Gly) rs535825137 0.00076
NM_001918.5(DBT):c.*4273C>A rs12568926 0.00074
NM_000353.3(TAT):c.*682T>C rs118086978 0.00070
NM_020686.6(ABAT):c.*2629G>A rs186857840 0.00065
NM_020686.6(ABAT):c.267C>T (p.Asp89=) rs199666932 0.00057
NM_001918.5(DBT):c.*5969C>T rs141483625 0.00055
NM_000274.4(OAT):c.1311G>T (p.Leu437Phe) rs1800456 0.00054
NM_000137.4(FAH):c.181G>T (p.Val61Phe) rs151264725 0.00053
NM_183050.4(BCKDHB):c.*83C>T rs564127416 0.00052
NM_001918.5(DBT):c.*7307G>C rs182980145 0.00051
NM_002150.3(HPD):c.1005C>G (p.Ile335Met) rs137852868 0.00051
NM_015702.3(MMADHC):c.617A>G (p.Asn206Ser) rs138607412 0.00051
NM_000161.3(GCH1):c.*20C>T rs143111433 0.00049
NM_001918.5(DBT):c.1210-11T>A rs751951997 0.00049
NM_000161.3(GCH1):c.206C>T (p.Pro69Leu) rs56127440 0.00035
NM_002860.4(ALDH18A1):c.*734C>A rs184009046 0.00035
NM_012463.4(ATP6V0A2):c.1486G>A (p.Ala496Thr) rs143142641 0.00035
NM_000161.3(GCH1):c.*1479G>T rs533240612 0.00034
NM_001918.5(DBT):c.*6716C>G rs529415312 0.00033
NM_000161.3(GCH1):c.*1130C>G rs543818323 0.00031
NM_006623.4(PHGDH):c.296C>G (p.Pro99Arg) rs182600362 0.00030
NM_000320.3(QDPR):c.*103C>T rs117036858 0.00029
NM_005589.4(ALDH6A1):c.*2491G>T rs181822532 0.00029
NM_005589.4(ALDH6A1):c.*567C>T rs75199385 0.00029
NM_000156.6(GAMT):c.279C>T (p.Asp93=) rs144630886 0.00028
NM_000360.4(TH):c.627C>G (p.Ile209Met) rs202149985 0.00027
NM_000108.5(DLD):c.*1736T>C rs190655078 0.00025
NM_000281.4(PCBD1):c.*114G>A rs562433724 0.00025
NM_001352514.2(HLCS):c.*1324T>C rs141644229 0.00024
NM_001918.5(DBT):c.*7698C>T rs185528579 0.00024
NM_000161.3(GCH1):c.69C>T (p.Pro23=) rs767294964 0.00023
NM_001918.5(DBT):c.1210-8A>T rs535837017 0.00023
NM_005589.4(ALDH6A1):c.97T>A (p.Phe33Ile) rs182720934 0.00022
NM_020686.6(ABAT):c.*989T>C rs533930699 0.00021
NM_000353.3(TAT):c.*863G>A rs185984423 0.00020
NM_183050.4(BCKDHB):c.*2072C>T rs183153737 0.00020
NM_183050.4(BCKDHB):c.63G>T (p.Gly21=) rs368345065 0.00019
NM_183050.4(BCKDHB):c.987C>T (p.His329=) rs138670449 0.00019
NM_000170.3(GLDC):c.1581-5C>T rs184463452 0.00018
NM_001080.3(ALDH5A1):c.*1249T>A rs149522807 0.00017
NM_018368.4(LMBRD1):c.1192T>C (p.Tyr398His) rs185334169 0.00016
NM_000161.3(GCH1):c.*256A>G rs181674470 0.00014
NM_000709.4(BCKDHA):c.*134C>T rs150173947 0.00014
NM_001080.3(ALDH5A1):c.*1515C>T rs368136060 0.00014
NM_001080.3(ALDH5A1):c.62G>A (p.Gly21Asp) rs371923295 0.00014
NM_001918.5(DBT):c.747C>A (p.Gly249=) rs200612682 0.00013
NM_006623.4(PHGDH):c.743C>T (p.Ala248Val) rs201782441 0.00013
NM_058179.4(PSAT1):c.1008-11G>T rs200199574 0.00013
NM_000137.4(FAH):c.715A>T (p.Ile239Phe) rs144228661 0.00012
NM_000048.4(ASL):c.1278C>T (p.Cys426=) rs140770112 0.00011
NM_000156.6(GAMT):c.242C>T (p.Ala81Val) rs751099274 0.00009
NM_000161.2(GCH1):c.-169C>T rs538405738 0.00009
NM_004577.4(PSPH):c.*317G>A rs565399960 0.00009
NM_012463.4(ATP6V0A2):c.1698A>G (p.Gly566=) rs2271659 0.00008
NM_000161.3(GCH1):c.297C>T (p.Ala99=) rs776450369 0.00007
NM_000277.3(PAH):c.*144A>G rs375319584 0.00007
NM_000709.4(BCKDHA):c.288+10G>A rs376894084 0.00007
NM_018368.4(LMBRD1):c.636+14G>T rs376670737 0.00007
NM_000687.4(AHCY):c.663T>C (p.Tyr221=) rs58020044 0.00006
NM_012463.4(ATP6V0A2):c.*2485C>T rs144043973 0.00006
NM_020686.6(ABAT):c.*2074A>C rs191157077 0.00006
NM_000071.3(CBS):c.1494G>A (p.Arg498=) rs778800147 0.00005
NM_000161.3(GCH1):c.543T>G (p.Val181=) rs765670568 0.00005
NM_000108.5(DLD):c.*1876G>A rs142001971 0.00004
NM_000187.4(HGD):c.1027A>C (p.Met343Leu) rs755078457 0.00004
NM_001352514.2(HLCS):c.2583C>T (p.Phe861=) rs532108774 0.00004
NM_020686.6(ABAT):c.*539C>T rs548945558 0.00004
NM_001080.3(ALDH5A1):c.*1349A>G rs542892289 0.00003
NM_002150.3(HPD):c.1108G>A (p.Ala370Thr) rs142321451 0.00003
NM_000161.3(GCH1):c.195G>A (p.Glu65=) rs139350456 0.00002
NM_000156.6(GAMT):c.*136C>A rs566649324 0.00001
NM_000156.6(GAMT):c.182G>A (p.Gly61Glu) rs77168423 0.00001
NM_000170.3(GLDC):c.63C>A (p.Arg21=) rs372141443 0.00001
NM_000317.3(PTS):c.121G>A (p.Gly41Arg) rs372852903 0.00001
NM_000353.3(TAT):c.*1056G>C rs535439847 0.00001
NM_000360.4(TH):c.5C>T (p.Pro2Leu) rs139474171 0.00001
NM_000709.4(BCKDHA):c.*324G>A rs564517344 0.00001
NM_006721.4(ADK):c.66-24289G>A rs571962706 0.00001
NM_012463.4(ATP6V0A2):c.*2085C>G rs185883563 0.00001
NM_012463.4(ATP6V0A2):c.2294-4G>A rs551697992 0.00001
NM_020686.6(ABAT):c.*1311C>A rs532670980 0.00001
NM_000048.4(ASL):c.531C>A (p.Ala177=) rs201974677
NM_000048.4(ASL):c.656-5C>A rs201814807
NM_000071.3(CBS):c.1358+15C>G rs186497436
NM_000108.5(DLD):c.*470G>A rs111619940
NM_000161.3(GCH1):c.*1122A>T rs56126158
NM_000161.3(GCH1):c.*1176C>G rs113211390
NM_000170.3(GLDC):c.1545G>A (p.Arg515=) rs121964976
NM_000170.3(GLDC):c.2490G>T (p.Thr830=) rs145407593
NM_000187.4(HGD):c.474G>T (p.Pro158=) rs2293734
NM_000274.4(OAT):c.1138A>G (p.Ile380Val) rs545710763
NM_000277.2(PAH):c.-224G>A rs886048892
NM_000277.2(PAH):c.-460delG rs113191080
NM_000320.3(QDPR):c.-24G>T rs529698353
NM_000481.4(AMT):c.148G>T (p.Val50Leu) rs148917929
NM_001080.3(ALDH5A1):c.*2778del rs771652776
NM_001080.3(ALDH5A1):c.709G>T (p.Ala237Ser) rs62621664
NM_001352514.2(HLCS):c.*1589CAAA[2] rs201997019
NM_001352514.2(HLCS):c.1620+7del rs140568778
NM_001354304.2(PAH):c.-95-385_-95-382del rs147576673
NM_001482.3(GATM):c.*28C>T rs570994409
NM_001918.5(DBT):c.*2619G>A rs541064624
NM_001918.5(DBT):c.*2633AAAT[7] rs773873766
NM_001918.5(DBT):c.*3869del rs141830881
NM_002860.4(ALDH18A1):c.-120A>G rs181772739
NM_003748.4(ALDH4A1):c.*657del rs11311839
NM_003748.4(ALDH4A1):c.1086G>A (p.Pro362=) rs41310410
NM_004577.4(PSPH):c.-19-13dup rs368626187
NM_004577.4(PSPH):c.249A>C (p.Gln83His) rs73343757
NM_005589.4(ALDH6A1):c.*309G>A rs150950908
NM_005589.4(ALDH6A1):c.*599C>G rs113031892
NM_005589.4(ALDH6A1):c.112-31GTTT[5] rs370924173
NM_005589.4(ALDH6A1):c.853-11dup rs528185481
NM_015702.3(MMADHC):c.-145A>G rs12477482
NM_018368.4(LMBRD1):c.-88C>G rs557851763
NM_020686.6(ABAT):c.*1765TTCA[2] rs148513949
NM_020686.6(ABAT):c.*3039del rs766850207
NM_020686.6(ABAT):c.*3110_*3113del rs147433667
NM_183050.4(BCKDHB):c.*263C>A rs533006469

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