Total 80 pathogenic variants reported for Lesch-Nyhan syndrome 
Variant Name Variant Type Variant Genomic Location Clinical Significance Phenotype Condition Review Status ClinGen Allele dbSNP ID Variation/condition record
NM_000194.2(HPRT1):c.239A>T (p.Asp80Val) SNV
Germline		 ChrX:134475285 Likely pathogenic Partial hypoxanthine-guanine phosphoribosyltransferase deficiency
HPRT ARLINGTON
Partial hypoxanthine-guanine phosphoribosyltransferase deficiency
Lesch-Nyhan syndrome		 Criteria Provided
Single Submitter
 CA120888 rs_137852478

2 SubmittersRCV000010714RCV000010715RCV001851783
NM_000194.2(HPRT1):c.122T>C (p.Leu41Pro) SNV
Germline		 ChrX:134473453 Pathogenic; other Lesch-Nyhan syndrome
HPRT DETROIT		 No Assertion Criteria Provided
 CA120890 rs_137852480

1 SubmittersRCV000010722RCV000010723
NM_000194.2(HPRT1):c.222C>A (p.Phe74Leu) SNV
Germline		 ChrX:134475268 Pathogenic; other HPRT FLINT
Lesch-Nyhan syndrome		 No Assertion Criteria Provided
 CA120892 rs_137852481

1 SubmittersRCV000010727RCV000010726
NM_000194.2(HPRT1):c.580G>A (p.Asp194Asn) SNV
Germline		 ChrX:134498655 Pathogenic Lesch-Nyhan syndrome No Assertion Criteria Provided
 CA120893 rs_267606863

1 SubmittersRCV000010728
NM_000194.2(HPRT1):c.329C>T (p.Ser110Leu) SNV
Germline		 ChrX:134486475 Likely pathogenic Partial hypoxanthine-guanine phosphoribosyltransferase deficiency
HPRT LONDON
Partial hypoxanthine-guanine phosphoribosyltransferase deficiency
Lesch-Nyhan syndrome		 Criteria Provided
Single Submitter
 CA120894 rs_137852482

2 SubmittersRCV000010730RCV000010731RCV003764546
NM_000194.2(HPRT1):c.389T>A (p.Val130Asp) SNV
Germline		 ChrX:134490192 Pathogenic; other HPRT MIDLAND
Lesch-Nyhan syndrome		 No Assertion Criteria Provided
 CA120895 rs_137852483

1 SubmittersRCV000010735RCV000010734
NM_000194.2(HPRT1):c.481G>T (p.Ala161Ser) SNV
Germline		 ChrX:134493586 Likely pathogenic Partial hypoxanthine-guanine phosphoribosyltransferase deficiency
HPRT MILWAUKEE
Partial hypoxanthine-guanine phosphoribosyltransferase deficiency
Lesch-Nyhan syndrome		 Criteria Provided
Single Submitter
 CA120896 rs_137852484

2 SubmittersRCV000010736RCV000010737RCV003764547
NM_000194.2(HPRT1):c.595T>G (p.Phe199Val) SNV
Germline		 ChrX:134498670 Pathogenic; other Lesch-Nyhan syndrome
HPRT NEW BRITON		 No Assertion Criteria Provided
 CA120898 rs_137852486

1 SubmittersRCV000010740RCV000010741
NM_000194.2(HPRT1):c.209G>A (p.Gly70Glu) SNV
Germline		 ChrX:134475255 Pathogenic HPRT NEW HAVEN
Lesch-Nyhan syndrome
Partial hypoxanthine-guanine phosphoribosyltransferase deficiency
Lesch-Nyhan syndrome		 Criteria Provided
Single Submitter
 CA120899 rs_137852487

2 SubmittersRCV000010743RCV000010742RCV001851784
NM_000194.2(HPRT1):c.211G>C (p.Gly71Arg) SNV
Germline		 ChrX:134475257 Likely pathogenic HPRT YALE
Lesch-Nyhan syndrome
Condition: not provided		 Criteria Provided
Single Submitter
 CA120900 rs_137852488

2 SubmittersRCV000010745RCV000010744RCV000790697
NM_000194.3(HPRT1):c.325C>T (p.Gln109Ter) SNV
Germline		 ChrX:134486471 Pathogenic Lesch-Nyhan syndrome
Lesch-Nyhan syndrome
Partial hypoxanthine-guanine phosphoribosyltransferase deficiency		 Criteria Provided
Single Submitter
 CA254997 rs_137852489

2 SubmittersRCV000010746RCV000631414
NM_000194.3(HPRT1):c.610C>G (p.His204Asp) SNV
Germline		 ChrX:134500030 Likely pathogenic Lesch-Nyhan syndrome
Lesch-Nyhan syndrome
Partial hypoxanthine-guanine phosphoribosyltransferase deficiency		 Criteria Provided
Single Submitter
 CA254999 rs_137852490

2 SubmittersRCV000010747RCV001250108
NM_000194.3(HPRT1):c.134G>A (p.Arg45Lys) SNV
Germline		 ChrX:134473465 Pathogenic Lesch-Nyhan syndrome No Assertion Criteria Provided
 CA255000 rs_137852491

1 SubmittersRCV000010748
NM_000194.3(HPRT1):c.529G>T (p.Asp177Tyr) SNV
Germline		 ChrX:134498433 Pathogenic Lesch-Nyhan syndrome No Assertion Criteria Provided
 CA255001 rs_137852492

1 SubmittersRCV000010749
NM_000194.3(HPRT1):c.609+5G>A SNV
Germline		 ChrX:134498689 Likely pathogenic Lesch-Nyhan syndrome
Condition: not provided
HPRT1-related disorder		 Criteria Provided
Single Submitter
 rs_1569360139

3 SubmittersRCV000010754RCV001571220RCV004545723
NM_000194.3(HPRT1):c.532+5G>A SNV
Germline		 ChrX:134498441 Pathogenic Lesch-Nyhan syndrome No Assertion Criteria Provided
 rs_1569360089

1 SubmittersRCV000010756
NM_000194.3(HPRT1):c.28-2A>T SNV
Germline		 ChrX:134473357 Pathogenic Lesch-Nyhan syndrome
HPRT1-related disorder		 Criteria Provided
Single Submitter
 rs_1569354918

2 SubmittersRCV000010757RCV004549355
NM_000194.3(HPRT1):c.527C>T (p.Pro176Leu) SNV
Germline		 ChrX:134498431 Pathogenic Lesch-Nyhan syndrome No Assertion Criteria Provided
 CA255003 rs_137852493

1 SubmittersRCV000010758
NM_000194.2(HPRT1):c.151C>T (p.Arg51Ter) SNV
Germline		 ChrX:134475197 Pathogenic Lesch-Nyhan syndrome
HPRT FUJIMI
Condition: not provided
Partial hypoxanthine-guanine phosphoribosyltransferase deficiency
Lesch-Nyhan syndrome
Microcephaly		 Criteria Provided
Multiple Submitters
No Conflicts
 CA120902 rs_137852494

7 SubmittersRCV000010761RCV000010762RCV000153366RCV001224361RCV001252944
NM_000194.2(HPRT1):c.170T>C (p.Met57Thr) SNV
Germline		 ChrX:134475216 Pathogenic; other Lesch-nyhan syndrome, neurologic variant
HPRT MONTREAL
HPRT1-related disorder		 No Assertion Criteria Provided
 CA120904 rs_137852495

2 SubmittersRCV000010763RCV000010764RCV004545724
NM_000194.3(HPRT1):c.428T>A (p.Met143Lys) SNV
Germline		 ChrX:134493533 Pathogenic Lesch-Nyhan syndrome No Assertion Criteria Provided
 CA255004 rs_137852496

1 SubmittersRCV000010765
NM_000194.3(HPRT1):c.508C>T (p.Arg170Ter) SNV
Germline		 ChrX:134498412 Pathogenic/Likely pathogenic Lesch-Nyhan syndrome
Lesch-Nyhan syndrome
Partial hypoxanthine-guanine phosphoribosyltransferase deficiency		 Criteria Provided
Multiple Submitters
No Conflicts
 CA255005 rs_137852497

3 SubmittersRCV000010766RCV003764548
HPRT CHERMSIDE SNV
Germline		 ChrX:134493591 Pathogenic Lesch-Nyhan syndrome
HPRT CHERMSIDE
Partial hypoxanthine-guanine phosphoribosyltransferase deficiency
Lesch-Nyhan syndrome		 Criteria Provided
Single Submitter
 rs_2077673385

2 SubmittersRCV000010783RCV001255650RCV003764549
NM_000194.2(HPRT1):c.459T>G (p.Tyr153Ter) SNV
Germline		 ChrX:134493564 Pathogenic; other Lesch-Nyhan syndrome
HPRT PARIS		 No Assertion Criteria Provided
 CA120914 rs_137852505

1 SubmittersRCV000010793RCV000010794
NM_000194.3(HPRT1):c.143G>A (p.Arg48His) SNV
Germline		 ChrX:134475189 Pathogenic Lesch-nyhan syndrome, neurologic variant
Lesch-Nyhan syndrome
Partial hypoxanthine-guanine phosphoribosyltransferase deficiency
Condition: not provided
Partial hypoxanthine-guanine phosphoribosyltransferase deficiency
HPRT1-related disorder		 Criteria Provided
Multiple Submitters
No Conflicts
 CA128815 rs_387906725

6 SubmittersRCV000022877RCV000690811RCV001092162RCV001255647RCV003398561
NM_000194.3(HPRT1):c.486-1G>A SNV
Germline		 ChrX:134498389 Pathogenic Condition: not provided
Partial hypoxanthine-guanine phosphoribosyltransferase deficiency
Lesch-Nyhan syndrome		 Criteria Provided
Multiple Submitters
No Conflicts
 CA220478 rs_398123241

2 SubmittersRCV000078345RCV001854376
NM_000194.3(HPRT1):c.47G>T (p.Gly16Val) SNV
Germline		 ChrX:134473378 Pathogenic Lesch-Nyhan syndrome Criteria Provided
Single Submitter
 CA414711272 rs_1135401801

1 SubmittersRCV000496113
NM_000194.3(HPRT1):c.384+9C>T SNV
Germline		 ChrX:134486539 Conflicting classifications of pathogenicity not specified
Partial hypoxanthine-guanine phosphoribosyltransferase deficiency
Lesch-Nyhan syndrome		 Criteria Provided
Conflicting Classifications
 CA10521371 rs_748658007

2 SubmittersRCV000501452RCV001511369
NM_000194.3(HPRT1):c.368C>G (p.Ser123Ter) SNV
Germline		 ChrX:134486514 Pathogenic Lesch-Nyhan syndrome
Partial hypoxanthine-guanine phosphoribosyltransferase deficiency		 Criteria Provided
Single Submitter
 rs_369065223

1 SubmittersRCV000706332
NM_000194.3(HPRT1):c.610C>T (p.His204Tyr) SNV
Germline		 ChrX:134500030 Likely pathogenic Partial hypoxanthine-guanine phosphoribosyltransferase deficiency
Lesch-Nyhan syndrome		 Criteria Provided
Single Submitter
 rs_137852490

1 SubmittersRCV000810491
NM_000194.3(HPRT1):c.319-2A>G SNV
Germline		 ChrX:134486463 Pathogenic Partial hypoxanthine-guanine phosphoribosyltransferase deficiency
Lesch-Nyhan syndrome		 Criteria Provided
Single Submitter
 rs_1602745376

1 SubmittersRCV000800143
NM_000194.3(HPRT1):c.221T>G (p.Phe74Cys) SNV
Unknown		 ChrX:134475267 Pathogenic Lesch-Nyhan syndrome Criteria Provided
Single Submitter
 rs_1602741150

1 SubmittersRCV000990949
NM_000194.3(HPRT1):c.481G>A (p.Ala161Thr) SNV
Germline		 ChrX:134493586 Likely pathogenic Partial hypoxanthine-guanine phosphoribosyltransferase deficiency
Lesch-Nyhan syndrome		 Criteria Provided
Single Submitter
 rs_137852484

1 SubmittersRCV001051587
NM_000194.3(HPRT1):c.486-2A>G SNV
Germline		 ChrX:134498388 Pathogenic Partial hypoxanthine-guanine phosphoribosyltransferase deficiency
Lesch-Nyhan syndrome		 Criteria Provided
Single Submitter
 rs_2077687102

1 SubmittersRCV001063460
NM_000194.3(HPRT1):c.212G>T (p.Gly71Val) SNV
Germline		 ChrX:134475258 Pathogenic Partial hypoxanthine-guanine phosphoribosyltransferase deficiency
Lesch-Nyhan syndrome		 Criteria Provided
Single Submitter
 rs_2124291450

1 SubmittersRCV001387578
NM_000194.3(HPRT1):c.539G>A (p.Gly180Glu) SNV
Germline		 ChrX:134498614 Pathogenic Lesch-Nyhan syndrome No Assertion Criteria Provided
 rs_2124305307

1 SubmittersRCV001542504
NM_000194.3(HPRT1):c.118G>T (p.Gly40Ter) SNV
Germline		 ChrX:134473449 Pathogenic Partial hypoxanthine-guanine phosphoribosyltransferase deficiency
Lesch-Nyhan syndrome		 Criteria Provided
Single Submitter
 rs_2124290355

1 SubmittersRCV001889471
NM_000194.3(HPRT1):c.546A>G (p.Glu182=) SNV
Germline		 ChrX:134498621 Conflicting classifications of pathogenicity Partial hypoxanthine-guanine phosphoribosyltransferase deficiency
Lesch-Nyhan syndrome
HPRT1-related disorder		 Criteria Provided
Conflicting Classifications
 rs_2124305311

2 SubmittersRCV001996184RCV003408064
NM_000194.3(HPRT1):c.430C>T (p.Gln144Ter) SNV
Germline		 ChrX:134493535 Pathogenic Partial hypoxanthine-guanine phosphoribosyltransferase deficiency
Lesch-Nyhan syndrome		 Criteria Provided
Single Submitter
 rs_2124302024

1 SubmittersRCV001951336
NM_000194.3(HPRT1):c.134+1G>C SNV
Germline		 ChrX:134473466 Likely pathogenic Lesch-Nyhan syndrome Criteria Provided
Single Submitter
 rs_2124290378

1 SubmittersRCV002249075
NM_000194.3(HPRT1):c.384+1G>T SNV
Germline		 ChrX:134486531 Likely pathogenic Lesch-Nyhan syndrome Criteria Provided
Single Submitter
 rs_398123240

1 SubmittersRCV002249076
NM_000194.3(HPRT1):c.233T>C (p.Leu78Pro) SNV
Germline		 ChrX:134475279 Pathogenic Lesch-Nyhan syndrome Criteria Provided
Single Submitter
 rs_2124291470

1 SubmittersRCV002250052
NM_000194.3(HPRT1):c.1A>G (p.Met1Val) SNV
Germline		 ChrX:134460312 Pathogenic Lesch-Nyhan syndrome Criteria Provided
Single Submitter
 rs_2124280504

1 SubmittersRCV002274283
NM_000194.3(HPRT1):c.568G>T (p.Gly190Ter) SNV
Germline		 ChrX:134498643 Pathogenic Lesch-Nyhan syndrome Criteria Provided
Single Submitter

1 SubmittersRCV002471511
NM_000194.3(HPRT1):c.611A>T (p.His204Leu) SNV
Germline		 ChrX:134500031 Pathogenic Partial hypoxanthine-guanine phosphoribosyltransferase deficiency
Lesch-Nyhan syndrome		 Criteria Provided
Single Submitter

1 SubmittersRCV003050654
NM_000194.3(HPRT1):c.580G>T (p.Asp194Tyr) SNV
Germline		 ChrX:134498655 Likely pathogenic Lesch-Nyhan syndrome Criteria Provided
Single Submitter

1 SubmittersRCV003142331
NM_000194.3(HPRT1):c.28-2A>G SNV
Germline		 ChrX:134473357 Likely pathogenic Lesch-Nyhan syndrome No Assertion Criteria Provided

1 SubmittersRCV003444515
NM_000194.3(HPRT1):c.402+1229A>G SNV
Germline		 ChrX:134491434 Likely pathogenic Lesch-Nyhan syndrome
Partial hypoxanthine-guanine phosphoribosyltransferase deficiency		 Criteria Provided
Single Submitter

1 SubmittersRCV003783780
NM_000194.3(HPRT1):c.403G>T (p.Asp135Tyr) SNV
Germline		 ChrX:134493508 Pathogenic Lesch-Nyhan syndrome
Partial hypoxanthine-guanine phosphoribosyltransferase deficiency		 Criteria Provided
Single Submitter

1 SubmittersRCV003783781