ClinVar Miner

List of variants reported as benign for X-linked syndromic intellectual disability by Genome-Nilou Lab

Included ClinVar conditions (104):
Minimum submission review status: Collection method:
Minimum conflict level:
ClinVar version:
Total variants: 46
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HGVS dbSNP gnomAD frequency
NM_000828.4(GRIA3):c.-2G= rs58044961 1.00000
NM_031407.7(HUWE1):c.12177T>C (p.Gly4059=) rs426298 0.99420
NM_016032.4(ZDHHC9):c.487+15A>G rs2275605 0.92100
NM_005765.3(ATP6AP2):c.534+45G>C rs3112299 0.91713
NM_004187.5(KDM5C):c.2243+11G>T rs1977364 0.81756
NM_001015877.2(PHF6):c.139-47G>A rs5978001 0.75584
NM_080632.3(UPF3B):c.264-34G>A rs2428212 0.66050
NM_024528.4(NKAP):c.923+6C>T rs194302 0.60390
NM_007325.5(GRIA3):c.751-16T>C rs550640 0.58620
NM_006517.5(SLC16A2):c.1399+43T>G rs5937843 0.57946
NM_007325.5(GRIA3):c.1200T>C (p.Asn400=) rs502434 0.57798
NM_001032382.2(PQBP1):c.180-3C>T rs741932 0.57792
NM_006517.5(SLC16A2):c.97T>C (p.Ser33Pro) rs6647476 0.54054
NM_001415.4(EIF2S3):c.99C>T (p.His33=) rs36018672 0.51303
NM_004595.5(SMS):c.170+30C>T rs3747276 0.51062
NM_000489.6(ATRX):c.2785= (p.Glu929=) rs3088074 0.49116
NM_031407.7(HUWE1):c.2109A>G (p.Ser703=) rs6638360 0.40138
NM_006950.3(SYN1):c.510T>C (p.Asn170=) rs1142636 0.39391
NM_001081550.2(THOC2):c.3058-9C>T rs2072914 0.35686
NM_031407.7(HUWE1):c.5716+37T>G rs266786 0.34800
NM_020717.5(SHROOM4):c.3468A>G (p.Glu1156=) rs3747282 0.29345
NM_001039591.3(USP9X):c.3558+16T>C rs5918130 0.27842
NM_001081550.2(THOC2):c.2317-47A>G rs3764750 0.26774
NM_004586.3(RPS6KA3):c.798C>A (p.Leu266=) rs2230488 0.24795
NM_005120.3(MED12):c.4415+29T>C rs10521349 0.23097
NM_005120.3(MED12):c.736-8A>C rs62609586 0.22423
NM_005120.3(MED12):c.205-38C>T rs12850852 0.22082
NM_005120.3(MED12):c.3930A>C (p.Pro1310=) rs5030619 0.21992
NM_006013.5(RPL10):c.-24+3G>A rs915942 0.18464
NM_005120.3(MED12):c.3354+27G>C rs5030617 0.15058
NM_015107.3(PHF8):c.2650-35C>G rs7886772 0.13065
NM_005120.3(MED12):c.2422+30C>T rs2075790 0.12776
NM_004595.5(SMS):c.866-32T>C rs2071136 0.09321
NM_001184880.2(PCDH19):c.402C>A (p.Ile134=) rs41300169 0.06912
NM_019597.5(HNRNPH2):c.1320C>T (p.Asn440=) rs3027574 0.03836
NM_000489.6(ATRX):c.5579A>G (p.Asn1860Ser) rs45439799 0.00663
NM_001081550.2(THOC2):c.2481+42A>G rs780461608 0.00005
NM_020717.5(SHROOM4):c.3942+48T>C rs781925536 0.00001
NM_001081550.2(THOC2):c.769-20dup rs201356571
NM_002139.4(RBMX):c.-1C>A rs2011584
NM_007325.5(GRIA3):c.384dup (p.Phe129fs) rs2147282654
NM_020717.5(SHROOM4):c.3372_3383dup (p.Gln1125_Gln1128dup) rs201922875
NM_020717.5(SHROOM4):c.3393GGA[8] (p.Glu1151dup) rs143151534
NM_024528.4(NKAP):c.538+8T>A rs194308
NM_024528.4(NKAP):c.539-17A>T rs194307
NM_024528.4(NKAP):c.600ATC[1] (p.Ser202del) rs10577974

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