Total 54 pathogenic variants reported for Primary hypomagnesemia 
Variant Name Variant Type Variant Genomic Location Clinical Significance Phenotype Condition Review Status ClinGen Allele dbSNP ID Variation/condition record
NM_006580.4(CLDN16):c.235C>T (p.Arg79Ter) SNV
Germline		 Chr3:190404779 Pathogenic Primary hypomagnesemia
Condition: not provided		 Criteria Provided
Multiple Submitters
No Conflicts
 CA117857 rs_104893720

8 SubmittersRCV000006288RCV002512826
NM_006580.4(CLDN16):c.505G>A (p.Gly169Arg) SNV
Germline		 Chr3:190408436 Pathogenic Primary hypomagnesemia
Condition: not provided		 Criteria Provided
Multiple Submitters
No Conflicts
 CA117859 rs_104893721

3 SubmittersRCV000006289RCV001851693
NM_006580.4(CLDN16):c.361G>A (p.Gly121Arg) SNV
Germline		 Chr3:190404905 Pathogenic Primary hypomagnesemia Criteria Provided
Single Submitter
 CA117860 rs_104893722

2 SubmittersRCV000006290
NM_006580.4(CLDN16):c.383G>A (p.Gly128Asp) SNV
Germline		 Chr3:190408314 Pathogenic/Likely pathogenic Primary hypomagnesemia
Condition: not provided		 Criteria Provided
Multiple Submitters
No Conflicts
 CA117861 rs_104893723

4 SubmittersRCV000006291RCV005089191
NM_006580.4(CLDN16):c.2T>G (p.Met1Arg) SNV
Germline		 Chr3:190388331 Pathogenic Primary hypomagnesemia No Assertion Criteria Provided
 CA117862 rs_104893724

1 SubmittersRCV000006292
NM_006580.4(CLDN16):c.290T>C (p.Leu97Pro) SNV
Germline		 Chr3:190404834 Pathogenic Primary hypomagnesemia No Assertion Criteria Provided
 CA117863 rs_104893725

1 SubmittersRCV000006293
NM_006580.4(CLDN16):c.488G>A (p.Gly163Asp) SNV
Germline		 Chr3:190408419 Pathogenic Primary hypomagnesemia No Assertion Criteria Provided
 CA117865 rs_104893727

1 SubmittersRCV000006295
NM_006580.4(CLDN16):c.494C>T (p.Ser165Phe) SNV
Germline		 Chr3:190408425 Pathogenic Primary hypomagnesemia No Assertion Criteria Provided
 CA117866 rs_104893728

1 SubmittersRCV000006296
NM_006580.4(CLDN16):c.243G>T (p.Leu81Phe) SNV
Germline		 Chr3:190404787 Pathogenic Primary hypomagnesemia
Condition: not provided		 Criteria Provided
Multiple Submitters
No Conflicts
 CA117867 rs_104893729

7 SubmittersRCV000006297RCV001093267
NM_006580.4(CLDN16):c.242T>G (p.Leu81Trp) SNV
Germline		 Chr3:190404786 Pathogenic Primary hypomagnesemia No Assertion Criteria Provided
 CA117868 rs_104893730

1 SubmittersRCV000006298
NM_006580.4(CLDN16):c.224T>C (p.Leu75Pro) SNV
Germline		 Chr3:190404768 Pathogenic Primary hypomagnesemia
Condition: not provided		 Criteria Provided
Single Submitter
 CA117869 rs_104893731

2 SubmittersRCV000006299RCV001851694
NM_006580.4(CLDN16):c.140G>A (p.Trp47Ter) SNV
Germline		 Chr3:190402362 Pathogenic Primary hypomagnesemia No Assertion Criteria Provided
 CA117870 rs_104893732

1 SubmittersRCV000006300
NM_006580.4(CLDN16):c.453G>T (p.Leu151Phe) SNV
Germline		 Chr3:190408384 Pathogenic Primary hypomagnesemia No Assertion Criteria Provided
 CA355767057 rs_1577432849

1 SubmittersRCV000006301
NM_006580.4(CLDN16):c.621T>G (p.Tyr207Ter) SNV
Germline		 Chr3:190409949 Pathogenic Primary hypomagnesemia No Assertion Criteria Provided
 CA117874 rs_121908543

1 SubmittersRCV000006303
NM_006580.4(CLDN16):c.613A>T (p.Lys205Ter) SNV
Germline		 Chr3:190409941 Pathogenic Primary hypomagnesemia No Assertion Criteria Provided
 CA129189 rs_387906880

1 SubmittersRCV000023358
NM_006580.4(CLDN16):c.114+13C>G SNV
Germline		 Chr3:190388456 Conflicting classifications of pathogenicity Primary hypomagnesemia
Condition: not provided		 Criteria Provided
Conflicting Classifications
 CA2753744 rs_369250510

2 SubmittersRCV000315060RCV002057872
NM_006580.4(CLDN16):c.117G>A (p.Val39=) SNV
Germline		 Chr3:190402339 Conflicting classifications of pathogenicity Primary hypomagnesemia
Condition: not provided		 Criteria Provided
Conflicting Classifications
 CA2753763 rs_528344809

2 SubmittersRCV000369762RCV000921476
NM_006580.4(CLDN16):c.206C>T (p.Ala69Val) SNV
Germline		 Chr3:190402428 Likely pathogenic Primary hypomagnesemia Criteria Provided
Single Submitter
 CA2753786 rs_765256758

2 SubmittersRCV000656736
NM_006580.4(CLDN16):c.392G>A (p.Gly131Glu) SNV
Unknown		 Chr3:190408323 Pathogenic Primary hypomagnesemia No Assertion Criteria Provided
 CA355766931 rs_138308105

1 SubmittersRCV000678491
NM_006580.4(CLDN16):c.217+5G>A SNV
Germline		 Chr3:190402444 Pathogenic/Likely pathogenic Primary hypomagnesemia
Condition: not provided		 Criteria Provided
Multiple Submitters
No Conflicts
 CA2753790 rs_751959432

8 SubmittersRCV000853501RCV005092533
NM_006580.4(CLDN16):c.382G>C (p.Gly128Arg) SNV
Unknown		 Chr3:190404926 Likely pathogenic Primary hypomagnesemia Criteria Provided
Single Submitter
 CA355766290 rs_1577430815

1 SubmittersRCV000987375
NM_006580.4(CLDN16):c.477A>G (p.Gln159=) SNV
Germline		 Chr3:190408408 Conflicting classifications of pathogenicity Condition: not provided
Primary hypomagnesemia
Inborn genetic diseases		 Criteria Provided
Conflicting Classifications
 CA2753879 rs_532245223

3 SubmittersRCV001046384RCV005036329RCV004973283
NM_006580.4(CLDN16):c.437G>A (p.Arg146His) SNV
Germline		 Chr3:190408368 Pathogenic/Likely pathogenic Condition: not provided
Primary hypomagnesemia		 Criteria Provided
Multiple Submitters
No Conflicts
 CA2753875 rs_772241737

5 SubmittersRCV001093268RCV003142041
NM_006580.4(CLDN16):c.22A>G (p.Ile8Val) SNV
Germline		 Chr3:190388351 Conflicting classifications of pathogenicity Primary hypomagnesemia
Inborn genetic diseases		 Criteria Provided
Conflicting Classifications
 CA2753728 rs_145118503

3 SubmittersRCV001150244RCV004032782
NM_006580.4(CLDN16):c.192C>T (p.Tyr64=) SNV
Germline		 Chr3:190402414 Conflicting classifications of pathogenicity Primary hypomagnesemia
Condition: not provided		 Criteria Provided
Conflicting Classifications
 CA2753783 rs_199651054

2 SubmittersRCV001144095RCV003727906
NM_006580.4(CLDN16):c.575-7C>T SNV
Germline		 Chr3:190409896 Conflicting classifications of pathogenicity Primary hypomagnesemia
Condition: not provided		 Criteria Provided
Conflicting Classifications
 CA2753911 rs_757064470

2 SubmittersRCV001144098RCV005093635
NM_006580.4(CLDN16):c.458A>G (p.Asn153Ser) SNV
Germline		 Chr3:190408389 Conflicting classifications of pathogenicity Primary hypomagnesemia
Condition: not provided
Inborn genetic diseases
Clear cell carcinoma of kidney		 Criteria Provided
Conflicting Classifications
 CA2753877 rs_201367228

8 SubmittersRCV001281173RCV001879805RCV002570440RCV005909209
NM_006580.4(CLDN16):c.2T>C (p.Met1Thr) SNV
Germline		 Chr3:190388331 Conflicting classifications of pathogenicity Primary hypomagnesemia Criteria Provided
Conflicting Classifications
 CA355762540 rs_104893724

2 SubmittersRCV001329583
NM_006580.4(CLDN16):c.130C>T (p.Arg44Ter) SNV
Germline		 Chr3:190402352 Pathogenic/Likely pathogenic Primary hypomagnesemia
Condition: not provided		 Criteria Provided
Multiple Submitters
No Conflicts
 rs_753901053

3 SubmittersRCV005360371RCV006264465
NM_006580.4(CLDN16):c.236G>A (p.Arg79Gln) SNV
Germline		 Chr3:190404780 Pathogenic Primary hypomagnesemia No Assertion Criteria Provided
 CA89763237 rs_968906940

1 SubmittersRCV001564039
NM_006580.4(CLDN16):c.137T>C (p.Leu46Pro) SNV
Germline		 Chr3:190402359 Likely pathogenic Primary hypomagnesemia Criteria Provided
Single Submitter
 CA355765476 rs_2108670592

2 SubmittersRCV001568363
NM_006580.4(CLDN16):c.103G>A (p.Asp35Asn) SNV
Germline		 Chr3:190388432 Likely pathogenic Primary hypomagnesemia Criteria Provided
Single Submitter
 CA355762807 rs_2108658339

2 SubmittersRCV001568368
NM_006580.4(CLDN16):c.149G>A (p.Cys50Tyr) SNV
Germline		 Chr3:190402371 Conflicting classifications of pathogenicity Condition: not provided
Primary hypomagnesemia		 Criteria Provided
Conflicting Classifications
 CA2753769 rs_149965853

3 SubmittersRCV001758778RCV005624492
NM_006580.4(CLDN16):c.494C>A (p.Ser165Tyr) SNV
Germline		 Chr3:190408425 Likely pathogenic Primary hypomagnesemia Criteria Provided
Single Submitter
 CA355767154 rs_104893728

1 SubmittersRCV001780794
NM_006580.4(CLDN16):c.217+1G>A SNV
Germline		 Chr3:190402440 Likely pathogenic Condition: not provided
Primary hypomagnesemia		 Criteria Provided
Multiple Submitters
No Conflicts
 CA355765852 rs_1718987504

2 SubmittersRCV002048920RCV005025679
NM_006580.4(CLDN16):c.-23A>G SNV
Germline		 Chr3:190388307 Conflicting classifications of pathogenicity Condition: not provided
Inborn genetic diseases
Primary hypomagnesemia		 Criteria Provided
Conflicting Classifications
 CA2753720 rs_752230428

3 SubmittersRCV001952755RCV004612018RCV005023482
NM_006580.4(CLDN16):c.487G>T (p.Gly163Cys) SNV
Germline		 Chr3:190408418 Likely pathogenic Condition: not provided
Primary hypomagnesemia		 Criteria Provided
Multiple Submitters
No Conflicts
 CA355767138 rs_1577432872

2 SubmittersRCV002226068RCV002502045
NM_006580.4(CLDN16):c.207G>A (p.Ala69=) SNV
Germline		 Chr3:190402429 Conflicting classifications of pathogenicity Condition: not provided
Primary hypomagnesemia		 Criteria Provided
Conflicting Classifications
 CA2753787 rs_137882210

2 SubmittersRCV002590570RCV005025886
NM_006580.4(CLDN16):c.574+2T>C SNV
Germline		 Chr3:190408507 Likely pathogenic Primary hypomagnesemia Criteria Provided
Single Submitter
 CA355767552 rs_2473800393

1 SubmittersRCV003994626
NM_006580.4(CLDN16):c.374T>C (p.Leu125Pro) SNV
Germline		 Chr3:190404918 Pathogenic Primary hypomagnesemia Criteria Provided
Single Submitter
 rs_1007522348

1 SubmittersRCV004585142
NM_006580.4(CLDN16):c.436C>T (p.Arg146Cys) SNV
Germline		 Chr3:190408367 Pathogenic/Likely pathogenic Primary hypomagnesemia Criteria Provided
Multiple Submitters
No Conflicts

3 SubmittersRCV004760306
NM_006580.4(CLDN16):c.152T>G (p.Val51Gly) SNV
Germline		 Chr3:190402374 Pathogenic Thrombocytopenia 5
Primary hypomagnesemia		 Criteria Provided
Single Submitter

1 SubmittersRCV004813329RCV005860449
NM_006580.4(CLDN16):c.3G>A (p.Met1Ile) SNV
Germline		 Chr3:190388332 Likely pathogenic Primary hypomagnesemia Criteria Provided
Single Submitter

1 SubmittersRCV005035294
NM_006580.4(CLDN16):c.236G>T (p.Arg79Leu) SNV
Germline		 Chr3:190404780 Likely pathogenic Primary hypomagnesemia Criteria Provided
Single Submitter

1 SubmittersRCV005024572
NM_006580.4(CLDN16):c.128G>T (p.Cys43Phe) SNV
Germline		 Chr3:190402350 Likely pathogenic Primary hypomagnesemia Criteria Provided
Single Submitter

1 SubmittersRCV005624655
NM_006580.4(CLDN16):c.83G>A (p.Cys28Tyr) SNV
Germline		 Chr3:190388412 Likely pathogenic Primary hypomagnesemia Criteria Provided
Single Submitter

1 SubmittersRCV005624656
NM_006580.4(CLDN16):c.498T>A (p.Cys166Ter) SNV
Germline		 Chr3:190408429 Likely pathogenic Primary hypomagnesemia Criteria Provided
Single Submitter

1 SubmittersRCV005636265
NM_006580.4(CLDN16):c.211C>G (p.His71Asp) SNV
Germline		 Chr3:190402433 Likely pathogenic Primary hypomagnesemia Criteria Provided
Single Submitter

1 SubmittersRCV006250102