ClinVar Miner

List of variants reported as pathogenic for autosomal recessive non-syndromic intellectual disability by OMIM

Included ClinVar conditions (71):
Minimum submission review status: Collection method:
Minimum conflict level:
ClinVar version:
Total variants: 194
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HGVS dbSNP gnomAD frequency
NM_181503.3(EXOSC8):c.815G>C (p.Ser272Thr) rs36027220 0.00400
NM_016042.4(EXOSC3):c.238G>T (p.Val80Phe) rs374550999 0.00093
NM_003754.3(EIF3F):c.694T>G (p.Phe232Val) rs141976414 0.00080
NM_003805.5(CRADD):c.509G>A (p.Arg170His) rs141179774 0.00053
NM_016042.4(EXOSC3):c.395A>C (p.Asp132Ala) rs141138948 0.00048
NM_153747.2(PIGC):c.61C>T (p.Arg21Ter) rs115209243 0.00031
NM_015275.3(WASHC4):c.1508A>G (p.His503Arg) rs201428088 0.00029
NM_003384.3(VRK1):c.1072C>T (p.Arg358Ter) rs137853063 0.00006
NM_014026.6(DCPS):c.260C>T (p.Thr87Met) rs138737928 0.00006
NM_014026.6(DCPS):c.947C>T (p.Thr316Met) rs137941190 0.00006
NM_015275.3(WASHC4):c.3236A>G (p.Lys1079Arg) rs748436953 0.00006
NM_003805.5(CRADD):c.382G>C (p.Gly128Arg) rs387906861 0.00005
NM_005883.3(APC2):c.1063G>A (p.Val355Ile) rs751785909 0.00005
NM_016219.5(MAN1B1):c.1000C>T (p.Arg334Cys) rs387906886 0.00005
NM_020374.4(C12orf4):c.983T>C (p.Leu328Pro) rs1468772495 0.00005
NM_001160372.4(TRAPPC9):c.1414C>T (p.Arg472Ter) rs267607137 0.00003
NM_001271838.2(RSRC1):c.205C>T (p.Arg69Ter) rs868818936 0.00003
NM_003805.5(CRADD):c.491T>G (p.Phe164Cys) rs370916968 0.00003
NM_016219.5(MAN1B1):c.1833_1834del (p.Asp613fs) rs1382373816 0.00003
NM_032808.7(LINGO1):c.869G>A (p.Arg290His) rs757077698 0.00003
NM_014026.6(DCPS):c.636+1G>A rs770528538 0.00002
NM_016042.4(EXOSC3):c.92G>C (p.Gly31Ala) rs387907196 0.00002
NM_018255.4(ELP2):c.1384C>T (p.Arg462Trp) rs767713084 0.00002
NM_145886.4(PIDD1):c.2584C>T (p.Arg862Trp) rs747620551 0.00002
NM_001160372.4(TRAPPC9):c.1129C>T (p.Arg377Ter) rs267607136 0.00001
NM_001543.5(NDST1):c.1831G>A (p.Gly611Ser) rs606231459 0.00001
NM_003384.3(VRK1):c.397C>T (p.Arg133Cys) rs387906830 0.00001
NM_003805.5(CRADD):c.508C>T (p.Arg170Cys) rs749655461 0.00001
NM_004830.4(MED23):c.1832G>A (p.Arg611Gln) rs370667926 0.00001
NM_004830.4(MED23):c.382G>A (p.Gly128Arg) rs569927513 0.00001
NM_006279.5(ST3GAL3):c.1046C>T (p.Thr349Met) rs1201878175 0.00001
NM_006828.4(ASCC3):c.5693A>G (p.His1898Arg) rs1381176199 0.00001
NM_016042.4(EXOSC3):c.415G>C (p.Ala139Pro) rs387907195 0.00001
NM_016219.5(MAN1B1):c.1189G>A (p.Glu397Lys) rs387906885 0.00001
NM_016219.5(MAN1B1):c.172G>T (p.Glu58Ter) rs753503405 0.00001
NM_016302.4(CRBN):c.1255C>T (p.Arg419Ter) rs121918368 0.00001
NM_017755.6(NSUN2):c.2035G>A (p.Gly679Arg) rs587776908 0.00001
NM_018255.4(ELP2):c.617A>G (p.His206Arg) rs773432002 0.00001
NM_020374.4(FERRY3):c.1360C>T (p.Arg454Ter) rs749969789 0.00001
NM_024989.4(PGAP1):c.1396C>T (p.Gln466Ter) rs143038880 0.00001
NM_032808.7(LINGO1):c.863A>G (p.Tyr288Cys) rs750612085 0.00001
NM_145886.4(PIDD1):c.2443C>T (p.Arg815Trp) rs758859772 0.00001
NM_153747.2(PIGC):c.635T>C (p.Leu212Pro) rs1553259602 0.00001
GRIK2, DEL/INV, EX7-11
NM_000827.4(GRIA1):c.1129C>T (p.Arg377Ter) rs1173036683
NM_001040616.3(LINS1):c.1219_1222+1del rs587777226
NM_001040616.3(LINS1):c.985_988del (p.His328_His329insTer) rs587777225
NM_001080510.5(METTL23):c.169_172del (p.His57fs) rs587777644
NM_001080510.5(METTL23):c.178dup (p.Glu60fs) rs1382444181
NM_001080510.5(METTL23):c.282_286del (p.Gln94fs) rs587777645
NM_001080510.5(METTL23):c.397C>T (p.Gln133Ter) rs587777646
NM_001136035.4(TRMT1):c.1332_1333del (p.Tyr445fs) rs1203487591
NM_001136035.4(TRMT1):c.1506+1G>T rs1568361011
NM_001136035.4(TRMT1):c.657_688del (p.Gln219fs) rs746572548
NM_001160372.4(TRAPPC9):c.2019_2022del (p.Leu674fs) rs2131714307
NM_001160372.4(TRAPPC9):c.2557-2A>C rs1587520018
NM_001271838.2(RSRC1):c.268C>T (p.Arg90Ter) rs1183090232
NM_001271838.2(RSRC1):c.3G>T (p.Met1Ile) rs1335486803
NM_001271838.2(RSRC1):c.441_447dup (p.Glu150fs) rs2108279740
NM_001271838.2(RSRC1):c.532-1G>A rs754550509
NM_001543.5(NDST1):c.1918T>C (p.Phe640Leu) rs606231458
NM_001543.5(NDST1):c.1926G>T (p.Glu642Asp) rs606231457
NM_001543.5(NDST1):c.2126G>A (p.Arg709Gln) rs606231456
NM_003292.3(TPR):c.2610+5G>A
NM_003292.3(TPR):c.6625C>T (p.Arg2209Ter)
NM_003619.4(PRSS12):c.1355_1358del (p.Asp452fs) rs876657372
NM_003754.3(EIF3F):c.861dup (p.Gln288fs) rs2133674310
NM_004830.4(MED23):c.1919A>G (p.Gln640Arg) rs745997916
NM_004830.4(MED23):c.3638A>G (p.His1213Arg) rs527236035
NM_004830.4(MED23):c.3988C>T (p.Arg1330Ter) rs527236036
NM_004830.4(MED23):c.506A>G (p.Tyr169Cys) rs2114757071
NM_004830.4(MED23):c.539C>A (p.Ala180Asp) rs2114756866
NM_004830.4(MED23):c.670C>G (p.Arg224Gly) rs1293450628
NM_005536.4(IMPA1):c.489_493dup (p.Ser165fs) rs1057519491
NM_005645.4(TAF13):c.119T>A (p.Met40Lys) rs1060505029
NM_005645.4(TAF13):c.92T>A (p.Leu31His) rs1060505030
NM_005883.3(APC2):c.5199dup (p.Lys1734fs) rs886040957
NM_005883.3(APC2):c.6620C>T (p.Pro2207Leu) rs1338563418
NM_006279.5(ST3GAL3):c.1108G>T (p.Asp370Tyr) rs1557612719
NM_006279.5(ST3GAL3):c.38C>A (p.Ala13Asp) rs387906943
NM_006618.5(KDM5B):c.3799del (p.Gln1267fs) rs1558479778
NM_006618.5(KDM5B):c.4109T>G (p.Leu1370Ter) rs1558478047
NM_006618.5(KDM5B):c.622dup (p.Tyr208fs) rs1558501648
NM_006618.5(KDM5B):c.787C>T (p.Pro263Ser) rs375695605
NM_006721.4(ADK):c.704A>C (p.Asp235Ala) rs397514453
NM_006721.4(ADK):c.89G>A (p.Gly30Glu) rs397514454
NM_006721.4(ADK):c.953C>A (p.Ala318Glu) rs397514452
NM_006765.4(TUSC3):c.163C>T (p.Gln55Ter) rs387906804
NM_006765.4(TUSC3):c.225del (p.Lys75fs) rs1554461593
NM_006765.4(TUSC3):c.786dup (p.Asn263fs) rs1585215916
NM_006828.4(ASCC3):c.3434del (p.Lys1145fs) rs759097017
NM_006828.4(ASCC3):c.3522dup (p.Cys1175fs)
NM_006828.4(ASCC3):c.3631C>T (p.Gln1211Ter)
NM_006828.4(ASCC3):c.4280C>T (p.Thr1427Met)
NM_006828.4(ASCC3):c.4415G>A (p.Arg1472Gln)
NM_006828.4(ASCC3):c.4553G>A (p.Arg1518His)
NM_006828.4(ASCC3):c.4690T>C (p.Ser1564Pro)
NM_006828.4(ASCC3):c.4955G>A (p.Gly1652Asp)
NM_006828.4(ASCC3):c.4984A>T (p.Ile1662Phe)
NM_006828.4(ASCC3):c.5281C>T (p.Arg1761Ter)
NM_006828.4(ASCC3):c.801+1G>T rs1432792609
NM_006895.3(HNMT):c.179G>A (p.Gly60Asp) rs758252808
NM_006895.3(HNMT):c.623T>C (p.Leu208Pro) rs745756308
NM_014026.6(DCPS):c.201+2T>C rs1057519083
NM_014168.4(METTL5):c.344_345del (p.Arg115fs) rs1573972562
NM_014168.4(METTL5):c.571_572del (p.Lys191fs) rs1573965358
NM_014415.4(ZBTB11):c.154C>T (p.Arg52Trp)
NM_014415.4(ZBTB11):c.2185C>T (p.His729Tyr) rs1559982532
NM_014415.4(ZBTB11):c.2640T>G (p.His880Gln) rs1559981249
NM_014415.4(ZBTB11):c.2668A>G (p.Thr890Ala)
NM_014415.4(ZBTB11):c.2708G>A (p.Arg903His)
NM_014415.4(ZBTB11):c.2734C>T (p.Arg912Trp)
NM_014415.4(ZBTB11):c.2779C>T (p.Arg927Ter)
NM_014415.4(ZBTB11):c.907A>T (p.Ile303Phe)
NM_014415.4:c.2977_2978del
NM_014704.4(CEP104):c.1901dup (p.Leu634fs) rs1411591918
NM_014704.4(CEP104):c.2356_2357insTT (p.Cys786fs) rs2124647615
NM_014704.4(CEP104):c.643C>T (p.Arg215Ter) rs759675006
NM_014806.5(RUSC2):c.2596C>T (p.Arg866Ter) rs1402086660
NM_014806.5(RUSC2):c.3952C>T (p.Arg1318Ter) rs1554645052
NM_015028.4(TNIK):c.538C>T (p.Arg180Ter) rs886037841
NM_015275.3(WASHC4):c.1324C>T (p.Gln442Ter) rs2135773055
NM_015275.3(WASHC4):c.3041A>G (p.Tyr1014Cys) rs768574664
NM_015275.3(WASHC4):c.3056C>G (p.Pro1019Arg) rs587777411
NM_015275.3(WASHC4):c.3143A>G (p.Asp1048Gly) rs1212552985
NM_015981.4(CAMK2A):c.1429C>T (p.His477Tyr) rs1554119274
NM_016042.4(EXOSC3):c.294_303del (p.Val99fs) rs672601331
NM_016042.4(EXOSC3):c.571G>T (p.Gly191Cys) rs730882145
NM_016042.4(EXOSC3):c.712T>C (p.Trp238Arg) rs672601332
NM_016100.5(NAA20):c.160A>G (p.Met54Val) rs2146464332
NM_016100.5(NAA20):c.239C>T (p.Ala80Val) rs768029717
NM_016219.5(MAN1B1):c.1225T>C (p.Ser409Pro) rs1158130828
NM_016219.5(MAN1B1):c.1311del (p.Leu438fs) rs747262065
NM_016219.5(MAN1B1):c.1418G>A (p.Trp473Ter) rs1564311909
NM_016219.5(MAN1B1):c.1445+2_1445+5del rs1831100970
NM_016219.5(MAN1B1):c.465+1462_620+529del
NM_016219.5(MAN1B1):c.530_542del (p.Leu177fs) rs797045688
NM_016219.5(MAN1B1):c.621-2A>G rs937318545
NM_016219.5(MAN1B1):c.761_764del (p.Ile254fs) rs1564281411
NM_016302.4(CRBN):c.1171T>C (p.Cys391Arg) rs797045036
NM_017721.5(CC2D1A):c.1223-294_1642-220del
NM_017755.6(NSUN2):c.1114C>T (p.Gln372Ter) rs387907191
NM_017755.6(NSUN2):c.538-11T>G rs2126499522
NM_017755.6(NSUN2):c.538-1G>C rs1560982564
NM_017755.6(NSUN2):c.679C>T (p.Gln227Ter) rs387907190
NM_018117.12(WDR11):c.1255C>T (p.Gln419Ter) rs2133748193
NM_018117.12(WDR11):c.1439del (p.Asn480fs) rs747938475
NM_018117.12(WDR11):c.2931+1G>A rs1252726486
NM_018117.12(WDR11):c.3033_3036del rs760973100
NM_018255.4(ELP2):c.1385G>T (p.Arg462Leu) rs371310428
NM_018255.4(ELP2):c.1663A>C (p.Thr555Pro) rs772450541
NM_020066.5(FMN2):c.1394dup (p.Ala466fs) rs727502860
NM_020066.5(FMN2):c.2515del (p.Thr839fs) rs727502861
NM_020374.4(FERRY3):c.639_640insACAA (p.Gln214fs) rs730882197
NM_021956.5(GRIK2):c.592C>T (p.Arg198Ter) rs749995448
NM_024298.5(MBOAT7):c.126_145del (p.Leu43fs) rs886041058
NM_024298.5(MBOAT7):c.423del (p.Leu142fs) rs886041059
NM_024298.5(MBOAT7):c.758_778del (p.Glu253_Ala259del) rs750035706
NM_024298.5(MBOAT7):c.820_826del (p.Gly274fs) rs886041061
NM_024298.5(MBOAT7):c.854+1G>C rs886041060
NM_024735.5(FBXO31):c.847_852delinsA (p.Cys283fs) rs587777703
NM_024824.5(ZC3H14):c.2204+17_2204+41del rs571303442
NM_024824.5(ZC3H14):c.460C>T (p.Arg154Ter) rs886037950
NM_024989.4(PGAP1):c.1090-2A>G rs869025581
NM_024989.4(PGAP1):c.1572T>A (p.Tyr524Ter) rs869025578
NM_024989.4(PGAP1):c.1952+1G>T rs587777202
NM_024989.4(PGAP1):c.274_276del (p.Pro92del) rs869025579
NM_024989.4(PGAP1):c.586CTT[1] (p.Leu197del) rs587777378
NM_024989.4(PGAP1):c.921_925del (p.Lys308fs) rs869025580
NM_025083.5(EDC3):c.161T>C (p.Phe54Ser) rs1057517676
NM_030805.4(LMAN2L):c.158G>A (p.Arg53Gln) rs869320632
NM_032982.4(CASP2):c.1156del (p.Tyr386fs)
NM_032982.4(CASP2):c.1174C>T (p.Gln392Ter)
NM_032982.4(CASP2):c.130C>T (p.Arg44Ter)
NM_032982.4(CASP2):c.876+1G>T
NM_138501.6(TECR):c.545C>T (p.Pro182Leu) rs199469705
NM_138775.3(ALKBH8):c.1651C>T (p.Arg551Ter) rs375189195
NM_138775.3(ALKBH8):c.1675del (p.Arg559fs)
NM_138775.3(ALKBH8):c.1785del (p.Trp596fs) rs1591234203
NM_145886.4(PIDD1):c.1804_1805del (p.Gly602fs) rs2133768184
NM_145886.4(PIDD1):c.2116_2120del (p.Val706fs) rs2133759109
NM_145886.4(PIDD1):c.2275-1G>A rs2133753509
NM_145886.4(PIDD1):c.2587C>T (p.Gln863Ter) rs1224174574
NM_152440.5(KICS2):c.1178A>G (p.Tyr393Cys)
NM_152440.5(KICS2):c.236-2del
NM_152440.5(KICS2):c.780del (p.Lys260fs)
NM_152440.5(KICS2):c.7G>T (p.Glu3Ter)
NM_152440.5(KICS2):c.888C>A (p.Asp296Glu)
NM_153747.2(PIGC):c.566T>G (p.Leu189Trp) rs1553259614
NM_181503.3(EXOSC8):c.5C>T (p.Ala2Val) rs606231285
NM_182543.5(NSUN6):c.1320_1323del (p.Glu441fs)
NM_182543.5(NSUN6):c.25_26del (p.Leu9fs) rs781644645
NM_182543.5(NSUN6):c.967G>A (p.Asp323Asn)
c.2475-2A-G

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