ClinVar Miner

List of variants studied for hereditary spastic paraplegia by Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

Included ClinVar conditions (140):
Minimum submission review status: Collection method:
Minimum conflict level:
ClinVar version:
Total variants: 116
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HGVS dbSNP gnomAD frequency
NM_003119.4(SPG7):c.1529C>T (p.Ala510Val) rs61755320 0.00361
NM_006612.6(KIF1C):c.2099C>T (p.Pro700Leu) rs148934699 0.00336
NM_003119.4(SPG7):c.1045G>A (p.Gly349Ser) rs141659620 0.00103
NM_001244008.2(KIF1A):c.3494T>C (p.Ile1165Thr) rs35698242 0.00063
NM_025137.4(SPG11):c.1384T>C (p.Cys462Arg) rs139019255 0.00058
NM_015346.4(ZFYVE26):c.5260G>A (p.Ala1754Thr) rs146968463 0.00045
NM_025137.4(SPG11):c.6625C>T (p.Arg2209Cys) rs374057859 0.00027
NM_001244008.2(KIF1A):c.4985G>A (p.Arg1662His) rs199557318 0.00026
NM_005186.4(CAPN1):c.221G>A (p.Gly74Asp) rs201318945 0.00026
NM_058004.4(PI4KA):c.2797A>G (p.Met933Val) rs142927362 0.00026
NM_003119.4(SPG7):c.1715C>T (p.Ala572Val) rs72547551 0.00015
NM_003119.4(SPG7):c.233T>A (p.Leu78Ter) rs121918358 0.00014
NM_004820.5(CYP7B1):c.101G>A (p.Cys34Tyr) rs1031580133 0.00014
NM_025137.4(SPG11):c.2318T>G (p.Val773Gly) rs182080501 0.00014
NM_001166114.2(PNPLA6):c.2939G>C (p.Gly980Ala) rs201902695 0.00011
NM_003119.4(SPG7):c.1672A>T (p.Lys558Ter) rs369227537 0.00010
NM_001010867.4(IBA57):c.679+3A>G rs754620334 0.00006
NM_014855.3(AP5Z1):c.1132G>A (p.Gly378Arg) rs777093701 0.00006
NM_014946.4(SPAST):c.250C>T (p.Arg84Cys) rs776114823 0.00006
NM_015346.4(ZFYVE26):c.3139+1G>A rs137907310 0.00006
NM_001166114.2(PNPLA6):c.4003C>T (p.Pro1335Ser) rs151264767 0.00005
NM_183075.3(CYP2U1):c.1376C>T (p.Pro459Leu) rs747965749 0.00005
NM_025137.4(SPG11):c.1348dup (p.Ile450fs) rs312262725 0.00004
NM_025137.4(SPG11):c.2003A>G (p.Tyr668Cys) rs764762491 0.00003
NM_025137.4(SPG11):c.6100C>T (p.Arg2034Ter) rs118203963 0.00003
NM_183075.3(CYP2U1):c.1462C>T (p.Arg488Trp) rs141431913 0.00003
NM_014855.3(AP5Z1):c.2352C>A (p.Asn784Lys) rs748913228 0.00002
NM_015214.3(DDHD2):c.724C>T (p.Arg242Cys) rs1380005347 0.00002
NM_015346.4(ZFYVE26):c.2539G>A (p.Ala847Thr) rs570114196 0.00002
NM_015346.4(ZFYVE26):c.3172C>T (p.Arg1058Trp) rs200775182 0.00002
NM_024306.5(FA2H):c.565C>T (p.Arg189Ter) rs765086319 0.00002
NM_001128126.3(AP4S1):c.306+4281A>G rs1228214819 0.00001
NM_001199753.2(CPT1C):c.449G>A (p.Trp150Ter) rs772980944 0.00001
NM_001253852.3(AP4B1):c.1216C>T (p.Arg406Ter) rs776976178 0.00001
NM_002860.4(ALDH18A1):c.1797G>C (p.Arg599Ser) rs752764884 0.00001
NM_004984.4(KIF5A):c.967C>T (p.Arg323Trp) rs1012819766 0.00001
NM_014855.3(AP5Z1):c.2399G>A (p.Arg800Lys) rs754594403 0.00001
NM_014855.3(AP5Z1):c.869G>A (p.Arg290Gln) rs778734781 0.00001
NM_024306.5(FA2H):c.965C>T (p.Ser322Leu) rs373010581 0.00001
NM_025137.4(SPG11):c.5866+1G>A rs765725393 0.00001
NM_025137.4(SPG11):c.6428A>C (p.His2143Pro) rs1490278448 0.00001
NM_000533.5(PLP1):c.214A>C (p.Ile72Leu)
NM_001010867.4(IBA57):c.262dup (p.Ala88fs) rs1558123212
NM_001130438.3(SPTAN1):c.55C>T (p.Arg19Trp) rs748232676
NM_001130438.3(SPTAN1):c.6031C>T (p.Arg2011Ter) rs2131938862
NM_001160148.2(DDHD1):c.1373G>A (p.Arg458Gln) rs1884724474
NM_001244008.2(KIF1A):c.2721GGA[10] (p.Glu917del) rs10594016
NM_001244008.2(KIF1A):c.3661del (p.Thr1221fs)
NM_001244008.2(KIF1A):c.821C>T (p.Ser274Leu) rs797045655
NM_001253852.3(AP4B1):c.1160_1161del (p.Thr387fs) rs587779388
NM_001253852.3(AP4B1):c.176C>G (p.Thr59Ser)
NM_001278116.2(L1CAM):c.1891G>T (p.Val631Leu)
NM_001278116.2(L1CAM):c.3755C>A (p.Pro1252His) rs2148491854
NM_001371279.1(REEP1):c.33-2A>G rs1574077569
NM_002860.4(ALDH18A1):c.2312T>C (p.Val771Ala)
NM_003119.4(SPG7):c.988-7C>T
NM_004181.5(UCHL1):c.250C>T (p.Gln84Ter) rs2154087189
NM_004722.4(AP4M1):c.1012del (p.Arg338fs) rs2116668499
NM_004984.4(KIF5A):c.1491C>G (p.Asn497Lys)
NM_004984.4(KIF5A):c.2175G>C (p.Gln725His)
NM_006612.6(KIF1C):c.1020G>A (p.Arg340=)
NM_006612.6(KIF1C):c.3256C>T (p.Arg1086Ter)
NM_014844.5(TECPR2):c.2846C>A (p.Ala949Glu)
NM_014844.5(TECPR2):c.480G>A (p.Gln160=)
NM_014846.4(WASHC5):c.3193C>T (p.Arg1065Ter)
NM_014855.3(AP5Z1):c.1573A>C (p.Lys525Gln) rs186003800
NM_014946.4(SPAST):c.1174G>C (p.Ala392Pro) rs1558331867
NM_014946.4(SPAST):c.1196C>T (p.Ser399Leu) rs1553317025
NM_014946.4(SPAST):c.1214del (p.Asn405fs)
NM_014946.4(SPAST):c.1245+5G>A rs1553317049
NM_014946.4(SPAST):c.1291C>T (p.Arg431Ter) rs786204126
NM_014946.4(SPAST):c.1378C>T (p.Arg460Cys) rs878854990
NM_014946.4(SPAST):c.1413+1G>A rs1553318276
NM_014946.4(SPAST):c.1413+3_1413+6del rs570685843
NM_014946.4(SPAST):c.1495C>T (p.Arg499Cys) rs121908511
NM_014946.4(SPAST):c.1496G>A (p.Arg499His) rs878854991
NM_014946.4(SPAST):c.1550T>G (p.Leu517Trp)
NM_014946.4(SPAST):c.1613C>A (p.Ala538Asp)
NM_014946.4(SPAST):c.1642G>C (p.Asp548His)
NM_014946.4(SPAST):c.1691del (p.Leu564fs) rs2148762771
NM_014946.4(SPAST):c.1714_1715del (p.Met572fs) rs2148762813
NM_014946.4(SPAST):c.870+1G>T rs1553314978
NM_015346.4(ZFYVE26):c.2254C>T (p.Gln752Ter) rs1057518016
NM_015346.4(ZFYVE26):c.2339G>A (p.Arg780Gln)
NM_015346.4(ZFYVE26):c.517del (p.Glu173fs)
NM_015346.4(ZFYVE26):c.5431C>T (p.Pro1811Ser) rs1012956419
NM_015915.5(ATL1):c.1306A>G (p.Asn436Asp) rs2140239163
NM_015915.5(ATL1):c.458G>C (p.Ser153Thr)
NM_015915.5(ATL1):c.574C>T (p.Leu192Phe) rs2039208042
NM_015915.5(ATL1):c.701A>T (p.Lys234Ile)
NM_016630.7(SPG21):c.226-1G>A
NM_020738.4(KIDINS220):c.2294A>G (p.Asn765Ser)
NM_020738.4(KIDINS220):c.256A>T (p.Ile86Phe)
NM_020738.4(KIDINS220):c.3395dup (p.His1133fs)
NM_020738.4(KIDINS220):c.4654G>A (p.Val1552Met)
NM_020738.4(KIDINS220):c.5032C>T (p.Arg1678Ter)
NM_020738.4(KIDINS220):c.959A>G (p.Asp320Gly)
NM_025137.4(SPG11):c.2444G>A (p.Arg815Lys)
NM_025137.4(SPG11):c.267G>A (p.Trp89Ter) rs312262709
NM_025137.4(SPG11):c.3037_3038+8del
NM_025137.4(SPG11):c.3074A>T (p.Lys1025Ile) rs1567163203
NM_025137.4(SPG11):c.5864del (p.Ser1955fs)
NM_025137.4(SPG11):c.6204A>G (p.Thr2068=)
NM_025137.4(SPG11):c.6754+2_6754+3dup rs759090170
NM_025137.4(SPG11):c.7205_7208del (p.Leu2402fs)
NM_058004.4(PI4KA):c.2386del (p.Arg796fs) rs1932452329
NM_058004.4(PI4KA):c.3109G>A (p.Ala1037Thr) rs1568988215
NM_058004.4(PI4KA):c.911T>A (p.Ile304Asn) rs752196534
NM_133443.4(GPT2):c.1481+3del
NM_133443.4(GPT2):c.328C>T (p.Arg110Trp)
NM_133443.4(GPT2):c.518G>C (p.Gly173Ala)
NM_133443.4(GPT2):c.839A>G (p.Lys280Arg)
NM_133443.4(GPT2):c.886C>T (p.Leu296Phe)
NM_133443.4(GPT2):c.935G>C (p.Arg312Thr)
NM_144599.5(NIPA1):c.257C>G (p.Ala86Gly)
NM_152415.3(VPS37A):c.1157C>T (p.Ala386Val)

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