Total 153 pathogenic variants reported for Lysinuric protein intolerance 
Variant Name Variant Type Variant Genomic Location Clinical Significance Phenotype Condition Review Status ClinGen Allele dbSNP ID Variation/condition record
NM_003982.4(SLC7A7):c.1A>C (p.Met1Leu) SNV
Germline		 Chr14:22813398 Pathogenic Lysinuric protein intolerance Criteria Provided
Single Submitter
 CA253799 rs_121908676

2 SubmittersRCV000006586
NM_003982.4(SLC7A7):c.1001T>G (p.Leu334Arg) SNV
Germline		 Chr14:22775538 Pathogenic Lysinuric protein intolerance Criteria Provided
Multiple Submitters
No Conflicts
 CA253804 rs_72552272

4 SubmittersRCV000006587
NM_003982.4(SLC7A7):c.1228C>T (p.Arg410Ter) SNV
Germline		 Chr14:22774371 Pathogenic Lysinuric protein intolerance Criteria Provided
Multiple Submitters
No Conflicts
 CA253812 rs_121908678

4 SubmittersRCV000006590
NM_003982.4(SLC7A7):c.726G>A (p.Trp242Ter) SNV
Germline		 Chr14:22778837 Pathogenic Lysinuric protein intolerance
Condition: not provided
Autoinflammatory syndrome		 Criteria Provided
Multiple Submitters
No Conflicts
 CA253817 rs_121908679

10 SubmittersRCV000006592RCV001723545RCV002262560
NM_001126105.2(SLC7A7):c.14C>T (p.Thr5Ile) SNV
Not provided		 Chr14:22813385 Likely pathogenic Lysinuric protein intolerance No Assertion Criteria Provided
 CA263748 rs_386833792

1 SubmittersRCV000049757
NM_001126105.2(SLC7A7):c.158C>T (p.Ser53Leu) SNV
Not provided		 Chr14:22813241 Likely pathogenic Lysinuric protein intolerance No Assertion Criteria Provided
 CA263752 rs_386833793

1 SubmittersRCV000049758
NM_003982.4(SLC7A7):c.1093A>T (p.Asn365Tyr) SNV
Not provided		 Chr14:22775446 Likely pathogenic Lysinuric protein intolerance No Assertion Criteria Provided
 CA263766 rs_386833797

1 SubmittersRCV000049762
NM_003982.4(SLC7A7):c.1158C>A (p.Ser386Arg) SNV
Not provided		 Chr14:22774441 Likely pathogenic Lysinuric protein intolerance No Assertion Criteria Provided
 CA263771 rs_386833799

1 SubmittersRCV000049764
NM_003982.4(SLC7A7):c.1371C>A (p.Tyr457Ter) SNV
Not provided		 Chr14:22773991 Likely pathogenic Lysinuric protein intolerance No Assertion Criteria Provided
 CA263783 rs_386833804

1 SubmittersRCV000049769
NM_003982.4(SLC7A7):c.1402C>T (p.Arg468Ter) SNV
Germline		 Chr14:22773960 Pathogenic/Likely pathogenic Lysinuric protein intolerance
Condition: not provided		 Criteria Provided
Multiple Submitters
No Conflicts
 CA263790 rs_386833807

8 SubmittersRCV000049772RCV003324723
NM_003982.4(SLC7A7):c.1417C>T (p.Arg473Ter) SNV
Germline		 Chr14:22773945 Pathogenic Lysinuric protein intolerance
Condition: not provided		 Criteria Provided
Multiple Submitters
No Conflicts
 CA263795 rs_386833808

9 SubmittersRCV000049773RCV001701733
NM_003982.4(SLC7A7):c.1465T>C (p.Ser489Pro) SNV
Not provided		 Chr14:22773681 Likely pathogenic Lysinuric protein intolerance No Assertion Criteria Provided
 CA263801 rs_386833810

1 SubmittersRCV000049775
NM_003982.4(SLC7A7):c.149T>A (p.Met50Lys) SNV
Germline		 Chr14:22813250 Likely pathogenic Lysinuric protein intolerance Criteria Provided
Multiple Submitters
No Conflicts
 CA263805 rs_386833811

3 SubmittersRCV000049776
NM_003982.4(SLC7A7):c.371T>C (p.Leu124Pro) SNV
Germline		 Chr14:22813028 Conflicting classifications of pathogenicity Lysinuric protein intolerance
not specified		 Criteria Provided
Conflicting Classifications
 CA263811 rs_386833814

3 SubmittersRCV000049779RCV001778694
NM_003982.4(SLC7A7):c.418G>C (p.Ala140Pro) SNV
Not provided		 Chr14:22812981 Likely pathogenic Lysinuric protein intolerance No Assertion Criteria Provided
 CA263815 rs_386833815

1 SubmittersRCV000049780
NM_003982.4(SLC7A7):c.454T>C (p.Phe152Leu) SNV
Not provided		 Chr14:22812945 Likely pathogenic Lysinuric protein intolerance No Assertion Criteria Provided
 CA263819 rs_386833816

1 SubmittersRCV000049781
NM_003982.4(SLC7A7):c.499+1G>A SNV
Germline		 Chr14:22812899 Pathogenic Lysinuric protein intolerance Criteria Provided
Single Submitter
 CA263823 rs_386833817

2 SubmittersRCV000049782
NM_003982.4(SLC7A7):c.563C>T (p.Thr188Ile) SNV
Not provided		 Chr14:22779988 Likely pathogenic Lysinuric protein intolerance No Assertion Criteria Provided
 CA263825 rs_386833819

1 SubmittersRCV000049784
NM_003982.4(SLC7A7):c.622C>T (p.Gln208Ter) SNV
Unknown		 Chr14:22779929 Pathogenic Lysinuric protein intolerance Criteria Provided
Single Submitter
 CA263833 rs_386833821

2 SubmittersRCV000049786
NM_003982.4(SLC7A7):c.625+1G>A SNV
Germline		 Chr14:22779925 Pathogenic Lysinuric protein intolerance
Condition: not provided
SLC7A7-related disorder		 Criteria Provided
Multiple Submitters
No Conflicts
 CA263838 rs_386833822

11 SubmittersRCV000049787RCV001547252RCV003415815
NM_003982.4(SLC7A7):c.625+1G>C SNV
Germline		 Chr14:22779925 Pathogenic Lysinuric protein intolerance Criteria Provided
Single Submitter
 CA263839 rs_386833822

2 SubmittersRCV000049788
NM_003982.4(SLC7A7):c.713C>T (p.Ser238Phe) SNV
Germline		 Chr14:22778850 Pathogenic/Likely pathogenic Lysinuric protein intolerance
Condition: not provided		 Criteria Provided
Multiple Submitters
No Conflicts
 CA263840 rs_386833823

6 SubmittersRCV000049789RCV002307385
NM_003982.4(SLC7A7):c.753G>T (p.Glu251Asp) SNV
Not provided		 Chr14:22778810 Likely pathogenic Lysinuric protein intolerance No Assertion Criteria Provided
 CA263844 rs_386833824

1 SubmittersRCV000049790
NM_003982.4(SLC7A7):c.782T>C (p.Leu261Pro) SNV
Not provided		 Chr14:22776307 Likely pathogenic Lysinuric protein intolerance No Assertion Criteria Provided
 CA263848 rs_386833825

1 SubmittersRCV000049791
NM_003982.4(SLC7A7):c.894+1G>T SNV
Germline		 Chr14:22776194 Pathogenic/Likely pathogenic Lysinuric protein intolerance Criteria Provided
Multiple Submitters
No Conflicts
 CA263853 rs_386833827

3 SubmittersRCV000049793
NM_003982.4(SLC7A7):c.895-2A>G SNV
Germline		 Chr14:22775938 Pathogenic Lysinuric protein intolerance Criteria Provided
Multiple Submitters
No Conflicts
 CA263854 rs_146582474

3 SubmittersRCV000049794
NM_003982.4(SLC7A7):c.998+1G>T SNV
Germline		 Chr14:22775832 Pathogenic Lysinuric protein intolerance Criteria Provided
Single Submitter
 CA263855 rs_386833828

2 SubmittersRCV000049795
NM_003982.4(SLC7A7):c.998G>T (p.Arg333Met) SNV
Germline		 Chr14:22775833 Likely pathogenic Lysinuric protein intolerance Criteria Provided
Single Submitter
 CA263856 rs_386833829

2 SubmittersRCV000049796
NM_003982.4(SLC7A7):c.475C>T (p.Arg159Cys) SNV
Germline		 Chr14:22812924 Conflicting classifications of pathogenicity Condition: not provided
Lysinuric protein intolerance
not specified
Autoinflammatory syndrome
Inborn genetic diseases		 Criteria Provided
Conflicting Classifications
 CA312994 rs_11568437

7 SubmittersRCV000186169RCV000279372RCV001778777RCV002262777RCV004020257
NM_003982.4(SLC7A7):c.720A>C (p.Ser240=) SNV
Germline		 Chr14:22778843 Conflicting classifications of pathogenicity Lysinuric protein intolerance
Condition: not provided
Autoinflammatory syndrome		 Criteria Provided
Conflicting Classifications
 CA7104619 rs_151261004

8 SubmittersRCV000329715RCV001706476RCV002262979
NM_003982.4(SLC7A7):c.342C>T (p.Phe114=) SNV
Germline		 Chr14:22813057 Conflicting classifications of pathogenicity Lysinuric protein intolerance Criteria Provided
Conflicting Classifications
 CA7104727 rs_777682875

3 SubmittersRCV000396241
NM_003982.4(SLC7A7):c.1128A>C (p.Glu376Asp) SNV
Germline		 Chr14:22774471 Conflicting classifications of pathogenicity Lysinuric protein intolerance
Autoinflammatory syndrome		 Criteria Provided
Conflicting Classifications
 CA7104471 rs_139619724

4 SubmittersRCV000304433RCV002262975
NM_003982.4(SLC7A7):c.1494T>C (p.Asp498=) SNV
Germline		 Chr14:22773652 Conflicting classifications of pathogenicity Lysinuric protein intolerance Criteria Provided
Conflicting Classifications
 CA7104367 rs_765682604

4 SubmittersRCV000278758
NM_003982.4(SLC7A7):c.931A>G (p.Ile311Val) SNV
Germline		 Chr14:22775900 Conflicting classifications of pathogenicity Lysinuric protein intolerance
Autoinflammatory syndrome		 Criteria Provided
Conflicting Classifications
 CA7104537 rs_539843065

4 SubmittersRCV000272643RCV002262978
NM_003982.4(SLC7A7):c.1095+6T>C SNV
Germline		 Chr14:22775438 Conflicting classifications of pathogenicity Lysinuric protein intolerance
Autoinflammatory syndrome		 Criteria Provided
Conflicting Classifications
 CA7104494 rs_531862402

4 SubmittersRCV000268955RCV002262976
NM_003982.4(SLC7A7):c.1064G>A (p.Arg355Gln) SNV
Germline		 Chr14:22775475 Conflicting classifications of pathogenicity Lysinuric protein intolerance
Autoinflammatory syndrome
SLC7A7-related disorder		 Criteria Provided
Conflicting Classifications
 CA7104499 rs_11568423

5 SubmittersRCV000326397RCV002262977RCV003969876
NM_003982.4(SLC7A7):c.339A>C (p.Gly113=) SNV
Germline		 Chr14:22813060 Conflicting classifications of pathogenicity Lysinuric protein intolerance
not specified		 Criteria Provided
Conflicting Classifications
 CA7104728 rs_139270936

6 SubmittersRCV000284819RCV000420340
NM_003982.4(SLC7A7):c.234C>T (p.Val78=) SNV
Germline		 Chr14:22813165 Conflicting classifications of pathogenicity Lysinuric protein intolerance
not specified
Condition: not provided		 Criteria Provided
Conflicting Classifications
 CA7104745 rs_139776370

8 SubmittersRCV000342178RCV000436290RCV001796740
NM_003982.4(SLC7A7):c.999G>A (p.Arg333=) SNV
Germline		 Chr14:22775540 Conflicting classifications of pathogenicity Condition: not provided
Lysinuric protein intolerance
Autoinflammatory syndrome		 Criteria Provided
Conflicting Classifications
 CA7104508 rs_146720775

9 SubmittersRCV000489698RCV000634956RCV002263700
NM_003982.4(SLC7A7):c.1122C>A (p.Cys374Ter) SNV
Germline		 Chr14:22774477 Pathogenic Lysinuric protein intolerance Criteria Provided
Multiple Submitters
No Conflicts
 rs_771254387

3 SubmittersRCV000680100
NM_003982.4(SLC7A7):c.894+6G>A SNV
Germline		 Chr14:22776189 Conflicting classifications of pathogenicity Lysinuric protein intolerance
SLC7A7-related disorder		 Criteria Provided
Conflicting Classifications
 rs_373812507

4 SubmittersRCV000686855RCV003945710
NM_003982.4(SLC7A7):c.549A>C (p.Val183=) SNV
Germline		 Chr14:22780002 Conflicting classifications of pathogenicity Lysinuric protein intolerance Criteria Provided
Conflicting Classifications
 rs_146945921

3 SubmittersRCV000920387
NM_003982.4(SLC7A7):c.123C>T (p.Asn41=) SNV
Germline		 Chr14:22813276 Conflicting classifications of pathogenicity Lysinuric protein intolerance Criteria Provided
Conflicting Classifications
 rs_367673752

4 SubmittersRCV000921859
NM_003982.4(SLC7A7):c.1263G>A (p.Pro421=) SNV
Germline		 Chr14:22774099 Conflicting classifications of pathogenicity Lysinuric protein intolerance Criteria Provided
Conflicting Classifications
 rs_1043886041

3 SubmittersRCV000975630
NM_003982.4(SLC7A7):c.895-2A>T SNV
Germline		 Chr14:22775938 Pathogenic Lysinuric protein intolerance Criteria Provided
Multiple Submitters
No Conflicts
 rs_146582474

7 SubmittersRCV001007644
NM_003982.4(SLC7A7):c.725G>A (p.Trp242Ter) SNV
Germline		 Chr14:22778838 Pathogenic/Likely pathogenic Lysinuric protein intolerance Criteria Provided
Multiple Submitters
No Conflicts
 rs_2038664064

2 SubmittersRCV001054857
NM_003982.4(SLC7A7):c.*272C>T SNV
Germline		 Chr14:22773338 Conflicting classifications of pathogenicity Lysinuric protein intolerance
Condition: not provided
Autoinflammatory syndrome		 Criteria Provided
Conflicting Classifications
 rs_143575981

3 SubmittersRCV001111463RCV001593273RCV002264186
NM_003982.4(SLC7A7):c.591G>A (p.Ala197=) SNV
Germline		 Chr14:22779960 Conflicting classifications of pathogenicity Lysinuric protein intolerance
Autoinflammatory syndrome		 Criteria Provided
Conflicting Classifications
 rs_750720946

3 SubmittersRCV001111558RCV002264187
NM_003982.4(SLC7A7):c.1246-12C>T SNV
Germline		 Chr14:22774128 Conflicting classifications of pathogenicity Lysinuric protein intolerance Criteria Provided
Conflicting Classifications
 rs_573454071

2 SubmittersRCV001114870
NM_003982.4(SLC7A7):c.439C>T (p.Leu147Phe) SNV
Germline		 Chr14:22812960 Conflicting classifications of pathogenicity Lysinuric protein intolerance
Inborn genetic diseases
Condition: not provided		 Criteria Provided
Conflicting Classifications
 rs_146280056

4 SubmittersRCV001279692RCV004035495RCV003481047
NM_003982.4(SLC7A7):c.770+1G>T SNV
Germline		 Chr14:22778792 Likely pathogenic Lysinuric protein intolerance Criteria Provided
Single Submitter
 rs_1264298481

1 SubmittersRCV001378639
NM_003982.4(SLC7A7):c.1116C>G (p.Tyr372Ter) SNV
Germline		 Chr14:22774483 Pathogenic/Likely pathogenic Lysinuric protein intolerance Criteria Provided
Multiple Submitters
No Conflicts
 rs_773357652

2 SubmittersRCV001384098
NM_003982.4(SLC7A7):c.766G>T (p.Glu256Ter) SNV
Germline		 Chr14:22778797 Pathogenic/Likely pathogenic Lysinuric protein intolerance Criteria Provided
Multiple Submitters
No Conflicts
 rs_2139394686

2 SubmittersRCV001382771
NM_003982.4(SLC7A7):c.88C>T (p.Gln30Ter) SNV
Germline		 Chr14:22813311 Pathogenic/Likely pathogenic Lysinuric protein intolerance Criteria Provided
Multiple Submitters
No Conflicts
 rs_2138663895

2 SubmittersRCV002000223
NM_003982.4(SLC7A7):c.930G>A (p.Trp310Ter) SNV
Germline		 Chr14:22775901 Pathogenic/Likely pathogenic Lysinuric protein intolerance Criteria Provided
Multiple Submitters
No Conflicts
 rs_2038594225

2 SubmittersRCV001924731
NM_003982.4(SLC7A7):c.465T>G (p.Tyr155Ter) SNV
Germline		 Chr14:22812934 Pathogenic Lysinuric protein intolerance Criteria Provided
Single Submitter
 rs_1029500488

1 SubmittersRCV001982912
NM_003982.4(SLC7A7):c.625+1G>T SNV
Germline		 Chr14:22779925 Pathogenic/Likely pathogenic Lysinuric protein intolerance Criteria Provided
Multiple Submitters
No Conflicts
 rs_386833822

2 SubmittersRCV001892901
NM_003982.4(SLC7A7):c.1A>G (p.Met1Val) SNV
Germline		 Chr14:22813398 Likely pathogenic Lysinuric protein intolerance Criteria Provided
Single Submitter

1 SubmittersRCV003072378
NM_003982.4(SLC7A7):c.3G>A (p.Met1Ile) SNV
Germline		 Chr14:22813396 Pathogenic Lysinuric protein intolerance Criteria Provided
Single Submitter

1 SubmittersRCV002791552
NM_003982.4(SLC7A7):c.1245+2T>C SNV
Germline		 Chr14:22774352 Likely pathogenic Lysinuric protein intolerance Criteria Provided
Single Submitter

1 SubmittersRCV002819440
NM_003982.4(SLC7A7):c.1429+2T>C SNV
Germline		 Chr14:22773931 Pathogenic Lysinuric protein intolerance Criteria Provided
Single Submitter

1 SubmittersRCV002815271
NM_003982.4(SLC7A7):c.501T>A (p.Cys167Ter) SNV
Germline		 Chr14:22780050 Pathogenic Lysinuric protein intolerance Criteria Provided
Single Submitter

1 SubmittersRCV002880492
NM_003982.4(SLC7A7):c.1281C>A (p.Cys427Ter) SNV
Germline		 Chr14:22774081 Pathogenic Lysinuric protein intolerance Criteria Provided
Single Submitter

1 SubmittersRCV002894604
NM_003982.4(SLC7A7):c.394C>T (p.Gln132Ter) SNV
Germline		 Chr14:22813005 Pathogenic Lysinuric protein intolerance Criteria Provided
Single Submitter

1 SubmittersRCV003016125
NM_003982.4(SLC7A7):c.894+1G>C SNV
Germline		 Chr14:22776194 Pathogenic Lysinuric protein intolerance Criteria Provided
Single Submitter

1 SubmittersRCV003047488
NM_003982.4(SLC7A7):c.1215G>A (p.Trp405Ter) SNV
Germline		 Chr14:22774384 Likely pathogenic Lysinuric protein intolerance Criteria Provided
Single Submitter

1 SubmittersRCV003234623
NM_003982.4(SLC7A7):c.1169G>A (p.Trp390Ter) SNV
Unknown		 Chr14:22774430 Likely pathogenic Lysinuric protein intolerance Criteria Provided
Single Submitter

1 SubmittersRCV003472947
NM_003982.4(SLC7A7):c.626-2A>T SNV
Unknown		 Chr14:22778939 Likely pathogenic Lysinuric protein intolerance Criteria Provided
Single Submitter

1 SubmittersRCV003472954
NM_003982.4(SLC7A7):c.94A>T (p.Lys32Ter) SNV
Unknown		 Chr14:22813305 Likely pathogenic Lysinuric protein intolerance Criteria Provided
Single Submitter

1 SubmittersRCV003474023
NM_003982.4(SLC7A7):c.1461T>A (p.Cys487Ter) SNV
Unknown		 Chr14:22773685 Likely pathogenic Lysinuric protein intolerance Criteria Provided
Single Submitter

1 SubmittersRCV003474024
NM_003982.4(SLC7A7):c.1371C>G (p.Tyr457Ter) SNV
Unknown		 Chr14:22773991 Likely pathogenic Lysinuric protein intolerance Criteria Provided
Single Submitter

1 SubmittersRCV003474031
NM_003982.4(SLC7A7):c.999-1G>C SNV
Unknown		 Chr14:22775541 Likely pathogenic Lysinuric protein intolerance Criteria Provided
Single Submitter

1 SubmittersRCV003474036
NM_003982.4(SLC7A7):c.21T>A (p.Tyr7Ter) SNV
Germline		 Chr14:22813378 Pathogenic Lysinuric protein intolerance Criteria Provided
Single Submitter

1 SubmittersRCV003508095
NM_003982.4(SLC7A7):c.770+1G>A SNV
Germline		 Chr14:22778792 Likely pathogenic Lysinuric protein intolerance Criteria Provided
Multiple Submitters
No Conflicts

2 SubmittersRCV003508251
NM_003982.4(SLC7A7):c.626-2A>G SNV
Germline		 Chr14:22778939 Likely pathogenic Lysinuric protein intolerance Criteria Provided
Single Submitter

1 SubmittersRCV003508866
NM_003982.4(SLC7A7):c.499+2T>G SNV
Germline		 Chr14:22812898 Likely pathogenic Lysinuric protein intolerance Criteria Provided
Single Submitter

1 SubmittersRCV003507889
NM_003982.4(SLC7A7):c.1429+1G>C SNV
Germline		 Chr14:22773932 Pathogenic Lysinuric protein intolerance Criteria Provided
Multiple Submitters
No Conflicts

2 SubmittersRCV003617141
NM_003982.4(SLC7A7):c.2T>C (p.Met1Thr) SNV
Germline		 Chr14:22813397 Likely pathogenic Lysinuric protein intolerance Criteria Provided
Single Submitter

1 SubmittersRCV003615541
NM_003982.4(SLC7A7):c.537G>A (p.Trp179Ter) SNV
Germline		 Chr14:22780014 Pathogenic Lysinuric protein intolerance Criteria Provided
Single Submitter

1 SubmittersRCV003878361
NM_003982.4(SLC7A7):c.305C>T (p.Ala102Val) SNV
Germline		 Chr14:22813094 Likely pathogenic Lysinuric protein intolerance Criteria Provided
Single Submitter

1 SubmittersRCV003990103
NM_003982.4(SLC7A7):c.1095+2T>G SNV
Unknown		 Chr14:22775442 Likely pathogenic Lysinuric protein intolerance Criteria Provided
Single Submitter

1 SubmittersRCV004573649