CLDN19 — 208 ClinVar variants
All ClinVar germline CLDN19 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 72 flagged for review →
9 Pathogenic · 3 Pathogenic/Likely pathogenic · 15 Likely pathogenic · 7 Conflicting · 13 Benign · 2 Benign/Likely benign · 47 Likely benign · 112 Uncertain significance
Full CLDN19 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 72
Variants where the independent computational evidence doesn't line up with the clinical picture — a QC signal for a second look, not a reclassification.
Predictors vs ClinVar 1
ClinVar calls these pathogenic, but the computational predictors lean tolerated — the highest-value review flag.
-
CLDN19 p.Gly75Ser
Pathogenic/Likely pathogenic
Multiple submitters
renal hypomagnesemia 5 with ocular involvement
Predictors agree, ClinVar conflicts 2
ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.
-
CLDN19 p.Gly179Ser
Conflicting
Single submitter
renal hypomagnesemia 5 with ocular involvement
-
CLDN19 p.Val176Met
Conflicting
Single submitter
Inborn genetic diseases
Predictors lean, ClinVar uncertain 48
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
-
CLDN19 p.Ala216Thr
Uncertain significance
Multiple submitters
renal hypomagnesemia 5 with ocular involvement
-
CLDN19 p.Ala218Thr
Uncertain significance
Multiple submitters
renal hypomagnesemia 5 with ocular involvement
-
CLDN19 p.Arg106Gln
Uncertain significance
Multiple submitters
renal hypomagnesemia 5 with ocular involvement
-
CLDN19 p.Arg208Gln
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
CLDN19 p.Asn193Lys
Uncertain significance
Multiple submitters
renal hypomagnesemia 5 with ocular involvement
-
CLDN19 p.Glu209Gly
Uncertain significance
Multiple submitters
renal hypomagnesemia 5 with ocular involvement
-
CLDN19 p.Leu50Ile
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
CLDN19 p.Leu50Phe
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
CLDN19 p.Ser69Leu
Uncertain significance
Multiple submitters
CLDN19-related disorder
-
CLDN19 p.Thr105Met
Uncertain significance
Multiple submitters
renal hypomagnesemia 5 with ocular involvement
-
CLDN19 p.Trp51Cys
Uncertain significance
Multiple submitters
renal hypomagnesemia 5 with ocular involvement
-
CLDN19 p.Ala121Thr
Uncertain significance
Single submitter
Inborn genetic diseases
-
CLDN19 p.Ala129Pro
Uncertain significance
Single submitter
renal hypomagnesemia 5 with ocular involvement
-
CLDN19 p.Ala136Val
Uncertain significance
Single submitter
Inborn genetic diseases
- CLDN19 p.Ala14Asp Uncertain significance Single submitter
-
CLDN19 p.Ala175Val
Uncertain significance
Single submitter
Inborn genetic diseases
-
CLDN19 p.Ala206Val
Uncertain significance
Single submitter
renal hypomagnesemia 5 with ocular involvement
- CLDN19 p.Ala207Thr Uncertain significance Single submitter
-
CLDN19 p.Ala36Ser
Uncertain significance
Single submitter
renal hypomagnesemia 5 with ocular involvement
-
CLDN19 p.Gln61Pro
Uncertain significance
Single submitter
Inborn genetic diseases
-
CLDN19 p.Glu147Lys
Uncertain significance
Single submitter
renal hypomagnesemia 5 with ocular involvement
-
CLDN19 p.Gly168Val
Uncertain significance
Single submitter
renal hypomagnesemia 5 with ocular involvement
-
CLDN19 p.Gly220Val
Uncertain significance
Single submitter
renal hypomagnesemia 5 with ocular involvement
-
CLDN19 p.Gly37Ser
Uncertain significance
Single submitter
Inborn genetic diseases
-
CLDN19 p.Gly60Arg
Uncertain significance
Single submitter
Inborn genetic diseases
-
CLDN19 p.Gly75Ala
Uncertain significance
Single submitter
Inborn genetic diseases
- CLDN19 p.Ile113Thr Uncertain significance Single submitter
-
CLDN19 p.Ile113Val
Uncertain significance
Single submitter
renal hypomagnesemia 5 with ocular involvement
-
CLDN19 p.Ile21Thr
Uncertain significance
Single submitter
Inborn genetic diseases
-
CLDN19 p.Lys219Glu
Uncertain significance
Single submitter
Inborn genetic diseases
-
CLDN19 p.Lys31Arg
Uncertain significance
Single submitter
Inborn genetic diseases
-
CLDN19 p.Met95Leu
Uncertain significance
Single submitter
Inborn genetic diseases
- CLDN19 p.Met95Val Uncertain significance Single submitter
-
CLDN19 p.Pro192Arg
Uncertain significance
Single submitter
Inborn genetic diseases
-
CLDN19 p.Pro221Leu
Uncertain significance
Single submitter
Inborn genetic diseases
-
CLDN19 p.Pro28Thr
Uncertain significance
Single submitter
Inborn genetic diseases
-
CLDN19 p.Ser152Asn
Uncertain significance
Single submitter
renal hypomagnesemia 5 with ocular involvement
-
CLDN19 p.Ser58Ile
Uncertain significance
Single submitter
renal hypomagnesemia 5 with ocular involvement
- CLDN19 p.Thr25Ile Uncertain significance Single submitter
-
CLDN19 p.Thr42Ala
Uncertain significance
Single submitter
renal hypomagnesemia 5 with ocular involvement
-
CLDN19 p.Tyr11His
Uncertain significance
Single submitter
renal hypomagnesemia 5 with ocular involvement
-
CLDN19 p.Tyr47Cys
Uncertain significance
Single submitter
renal hypomagnesemia 5 with ocular involvement
- CLDN19 p.Val137Phe Uncertain significance Single submitter
-
CLDN19 p.Val176Leu
Uncertain significance
Single submitter
renal hypomagnesemia 5 with ocular involvement
- CLDN19 p.Val44Leu Uncertain significance Single submitter
-
CLDN19 p.Val93Leu
Uncertain significance
Single submitter
renal hypomagnesemia 5 with ocular involvement
- CLDN19 p.Ala43Val Uncertain significance No assertion criteria
- CLDN19 p.Gly101Ser Uncertain significance No assertion criteria
Predictors split 21
The independent predictors disagree with each other — read with care.
-
CLDN19 p.Ala55Thr
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
CLDN19 p.Arg106Trp
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
CLDN19 p.Arg117Cys
Uncertain significance
Multiple submitters
renal hypomagnesemia 5 with ocular involvement
-
CLDN19 p.Arg117His
Uncertain significance
Multiple submitters
renal hypomagnesemia 5 with ocular involvement
-
CLDN19 p.Arg200Gln
Benign
Multiple submitters
renal hypomagnesemia 5 with ocular involvement
-
CLDN19 p.Gly220Cys
Uncertain significance
Multiple submitters
renal hypomagnesemia 5 with ocular involvement
-
CLDN19 p.Ile22Thr
Uncertain significance
Multiple submitters
renal hypomagnesemia 5 with ocular involvement
-
CLDN19 p.Leu13Phe
Benign/Likely benign
Multiple submitters
renal hypomagnesemia 5 with ocular involvement
-
CLDN19 p.Pro112Leu
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
CLDN19 p.Pro187Leu
Uncertain significance
Multiple submitters
renal hypomagnesemia 5 with ocular involvement
-
CLDN19 p.Val224Glu
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
CLDN19 p.Gly75Arg
Likely pathogenic
Single submitter
renal hypomagnesemia 5 with ocular involvement
-
CLDN19 p.Ile77Val
Conflicting
Single submitter
Inborn genetic diseases
-
CLDN19 p.Leu134Phe
Uncertain significance
Single submitter
renal hypomagnesemia 5 with ocular involvement
-
CLDN19 p.Pro187Ser
Uncertain significance
Single submitter
Inborn genetic diseases
-
CLDN19 p.Ser53Thr
Uncertain significance
Single submitter
Inborn genetic diseases
-
CLDN19 p.Thr145Ala
Uncertain significance
Single submitter
Inborn genetic diseases
- CLDN19 p.Val86Ala Uncertain significance Single submitter
-
CLDN19 p.Val88Met
Uncertain significance
Single submitter
Inborn genetic diseases
- CLDN19 p.Val93Met Conflicting Single submitter
-
CLDN19 p.Gln57Glu
Pathogenic
No assertion criteria
renal hypomagnesemia 5 with ocular involvement
All CLDN19 variants
Pathogenic 9
- p.Leu143fs Multiple submitters renal hypomagnesemia 5 with ocular involvement
- c.389-2A>G Single submitter
- c.474-1G>C Single submitter renal hypomagnesemia 5 with ocular involvement
- p.Tyr67Ter Single submitter
- p.Gln57Glu No assertion criteria renal hypomagnesemia 5 with ocular involvement ⚠
- p.Gln57Ter No assertion criteria renal hypomagnesemia 5 with ocular involvement
- p.Gln61Ter No assertion criteria renal hypomagnesemia 5 with ocular involvement
- p.Gly130Cys No assertion criteria renal hypomagnesemia 5 with ocular involvement
- p.Leu90Pro No assertion criteria renal hypomagnesemia 5 with ocular involvement
Pathogenic/Likely pathogenic 3
- p.Gly20Asp Multiple submitters renal hypomagnesemia 5 with ocular involvement
- p.Gly75Ser Multiple submitters renal hypomagnesemia 5 with ocular involvement ⚠
- p.Leu90Arg Multiple submitters renal hypomagnesemia 5 with ocular involvement
Likely pathogenic 15
- p.Pro28Leu Multiple submitters renal hypomagnesemia 5 with ocular involvement
- c.223+1G>A Single submitter renal hypomagnesemia 5 with ocular involvement
- c.474-1G>A Single submitter
- p.Arg81Trp Single submitter renal hypomagnesemia 5 with ocular involvement
- p.Asp74fs Single submitter renal hypomagnesemia 5 with ocular involvement
- p.Cys54Ter Single submitter renal hypomagnesemia 5 with ocular involvement
- p.Gly162Cys Single submitter renal hypomagnesemia 5 with ocular involvement
- p.Gly179Arg Single submitter renal hypomagnesemia 5 with ocular involvement
- p.Gly60fs Single submitter renal hypomagnesemia 5 with ocular involvement
- p.Gly75Arg Single submitter renal hypomagnesemia 5 with ocular involvement ⚠
- p.Gly91fs Single submitter renal hypomagnesemia 5 with ocular involvement
- p.Leu131Arg Single submitter renal hypomagnesemia 5 with ocular involvement
- p.Leu177Arg Single submitter renal hypomagnesemia 5 with ocular involvement
- p.Leu46_Tyr47insTer Single submitter renal hypomagnesemia 5 with ocular involvement
- p.Val88Glu Single submitter renal hypomagnesemia 5 with ocular involvement
Conflicting classifications of pathogenicity 7
- c.626+7C>A Single submitter renal hypomagnesemia 5 with ocular involvement
- p.Gly179Ser Single submitter renal hypomagnesemia 5 with ocular involvement ⚠
- p.Ile77Val Single submitter Inborn genetic diseases ⚠
- p.Leu143= Single submitter renal hypomagnesemia 5 with ocular involvement
- p.Phe166= Single submitter renal hypomagnesemia 5 with ocular involvement
- p.Val176Met Single submitter Inborn genetic diseases ⚠
- p.Val93Met Single submitter ⚠
Benign 13
- c.626+15C>T Multiple submitters renal hypomagnesemia 5 with ocular involvement
- c.626+333T>G Multiple submitters
- c.627-50C>T Multiple submitters
- c.*1642T>C Multiple submitters renal hypomagnesemia 5 with ocular involvement
- c.*1733G>A Multiple submitters renal hypomagnesemia 5 with ocular involvement
- c.*231A>G Multiple submitters renal hypomagnesemia 5 with ocular involvement
- c.*91A>G Multiple submitters renal hypomagnesemia 5 with ocular involvement
- p.Arg200Gln Multiple submitters renal hypomagnesemia 5 with ocular involvement ⚠
- p.Pro187= Multiple submitters renal hypomagnesemia 5 with ocular involvement
- c.*1018G>T Single submitter renal hypomagnesemia 5 with ocular involvement
- c.*1327T>C Single submitter renal hypomagnesemia 5 with ocular involvement
- c.*1760C>T Single submitter renal hypomagnesemia 5 with ocular involvement
- c.*873A>G Single submitter renal hypomagnesemia 5 with ocular involvement
Benign/Likely benign 2
- c.*158G>A Multiple submitters renal hypomagnesemia 5 with ocular involvement
- p.Leu13Phe Multiple submitters renal hypomagnesemia 5 with ocular involvement ⚠
Likely benign 47
- c.224-64C>A Multiple submitters
- c.626+75C>G Multiple submitters renal hypomagnesemia 5 with ocular involvement
- p.Ala43= Multiple submitters renal hypomagnesemia 5 with ocular involvement
- p.Gly178= Multiple submitters Inborn genetic diseases
- p.Thr185= Multiple submitters Inborn genetic diseases
- p.Tyr140= Multiple submitters
- c.223+11G>C Single submitter
- c.223+14C>T Single submitter
- c.223+15G>A Single submitter
- c.223+17C>T Single submitter
- c.223+20G>A Single submitter
- c.223+8C>T Single submitter
- c.223+9C>G Single submitter
- c.224-15T>A Single submitter
- c.224-189del Single submitter
- c.224-7A>T Single submitter
- c.388+14A>G Single submitter
- c.388+19T>A Single submitter
- c.474-167G>T Single submitter
- c.474-291A>G Single submitter
- c.474-6T>C Single submitter
- c.626+16G>A Single submitter
- c.627-20C>A Single submitter
- c.627-20C>G Single submitter
- c.627-36dup Single submitter
- c.-19C>T Single submitter renal hypomagnesemia 5 with ocular involvement
- c.*845C>G Single submitter renal hypomagnesemia 5 with ocular involvement
- p.Ala164= Single submitter Inborn genetic diseases
- p.Asp38= Single submitter
- p.Cys54= Single submitter
- p.Gln63= Single submitter
- p.Gly116= Single submitter
- p.Gly162= Single submitter
- p.Gly5= Single submitter
- p.Gly60= Single submitter
- p.Leu50= Single submitter
- p.Pro215= Single submitter
- p.Pro221= Single submitter
- p.Ser138= Single submitter
- p.Ser217= Single submitter
- p.Ser69= Single submitter
- p.Thr105= Single submitter
- p.Tyr11= Single submitter
- p.Tyr35= Single submitter
- p.Val176= Single submitter Inborn genetic diseases
- p.Val224= Single submitter
- p.Ala175= No assertion criteria CLDN19-related disorder
Uncertain significance 112
- c.-150C>T Multiple submitters renal hypomagnesemia 5 with ocular involvement
- p.Ala216Thr Multiple submitters renal hypomagnesemia 5 with ocular involvement ⚠
- p.Ala218Thr Multiple submitters renal hypomagnesemia 5 with ocular involvement ⚠
- p.Ala55Thr Multiple submitters Inborn genetic diseases ⚠
- p.Arg106Gln Multiple submitters renal hypomagnesemia 5 with ocular involvement ⚠
- p.Arg106Trp Multiple submitters Inborn genetic diseases ⚠
- p.Arg117Cys Multiple submitters renal hypomagnesemia 5 with ocular involvement ⚠
- p.Arg117His Multiple submitters renal hypomagnesemia 5 with ocular involvement ⚠
- p.Arg208Gln Multiple submitters Inborn genetic diseases ⚠
- p.Arg208Ter Multiple submitters renal hypomagnesemia 5 with ocular involvement
- p.Asn193Lys Multiple submitters renal hypomagnesemia 5 with ocular involvement ⚠
- p.Glu209Gly Multiple submitters renal hypomagnesemia 5 with ocular involvement ⚠
- p.Gly220Cys Multiple submitters renal hypomagnesemia 5 with ocular involvement ⚠
- p.Ile22Thr Multiple submitters renal hypomagnesemia 5 with ocular involvement ⚠
- p.Leu50Ile Multiple submitters Inborn genetic diseases ⚠
- p.Leu50Phe Multiple submitters Inborn genetic diseases ⚠
- p.Pro112Leu Multiple submitters Inborn genetic diseases ⚠
- p.Pro187Leu Multiple submitters renal hypomagnesemia 5 with ocular involvement ⚠
- p.Ser69Leu Multiple submitters CLDN19-related disorder ⚠
- p.Thr105Met Multiple submitters renal hypomagnesemia 5 with ocular involvement ⚠
- p.Trp51Cys Multiple submitters renal hypomagnesemia 5 with ocular involvement ⚠
- p.Val224Glu Multiple submitters Inborn genetic diseases ⚠
- c.223+3A>T Single submitter
- c.473+1G>T Single submitter renal hypomagnesemia 5 with ocular involvement
- c.473+8C>T Single submitter
- c.626+116G>C Single submitter Renal tubulopathies
- c.626+5G>A Single submitter renal hypomagnesemia 5 with ocular involvement
- c.-145C>T Single submitter renal hypomagnesemia 5 with ocular involvement
- c.-146G>A Single submitter renal hypomagnesemia 5 with ocular involvement
- c.*1008C>T Single submitter renal hypomagnesemia 5 with ocular involvement
- c.*1072C>T Single submitter renal hypomagnesemia 5 with ocular involvement
- c.*1073G>A Single submitter renal hypomagnesemia 5 with ocular involvement
- c.*1172C>T Single submitter renal hypomagnesemia 5 with ocular involvement
- c.*119C>T Single submitter renal hypomagnesemia 5 with ocular involvement
- c.*1312G>A Single submitter renal hypomagnesemia 5 with ocular involvement
- c.*1312G>T Single submitter renal hypomagnesemia 5 with ocular involvement
- c.*1336T>C Single submitter renal hypomagnesemia 5 with ocular involvement
- c.*1353G>A Single submitter renal hypomagnesemia 5 with ocular involvement
- c.*1357C>T Single submitter renal hypomagnesemia 5 with ocular involvement
- c.*1428A>G Single submitter renal hypomagnesemia 5 with ocular involvement
- c.*1483G>T Single submitter renal hypomagnesemia 5 with ocular involvement
- c.*1621T>C Single submitter renal hypomagnesemia 5 with ocular involvement
- c.*1698A>G Single submitter renal hypomagnesemia 5 with ocular involvement
- c.*1772A>C Single submitter renal hypomagnesemia 5 with ocular involvement
- c.*177C>A Single submitter renal hypomagnesemia 5 with ocular involvement
- c.*1822C>T Single submitter renal hypomagnesemia 5 with ocular involvement
- c.*1829A>G Single submitter renal hypomagnesemia 5 with ocular involvement
- c.*1908C>T Single submitter renal hypomagnesemia 5 with ocular involvement
- c.*1909G>A Single submitter renal hypomagnesemia 5 with ocular involvement
- c.*1919G>A Single submitter renal hypomagnesemia 5 with ocular involvement
- c.*1925T>C Single submitter renal hypomagnesemia 5 with ocular involvement
- c.*1965T>G Single submitter renal hypomagnesemia 5 with ocular involvement
- c.*19G>A Single submitter renal hypomagnesemia 5 with ocular involvement
- c.*257C>T Single submitter renal hypomagnesemia 5 with ocular involvement
- c.*285C>A Single submitter renal hypomagnesemia 5 with ocular involvement
- c.*45G>A Single submitter renal hypomagnesemia 5 with ocular involvement
- c.*491C>T Single submitter renal hypomagnesemia 5 with ocular involvement
- c.*523G>A Single submitter renal hypomagnesemia 5 with ocular involvement
- c.*547C>T Single submitter renal hypomagnesemia 5 with ocular involvement
- c.*598G>T Single submitter renal hypomagnesemia 5 with ocular involvement
- c.*624C>T Single submitter renal hypomagnesemia 5 with ocular involvement
- c.*639C>T Single submitter renal hypomagnesemia 5 with ocular involvement
- c.*642G>A Single submitter renal hypomagnesemia 5 with ocular involvement
- c.*735G>C Single submitter renal hypomagnesemia 5 with ocular involvement
- c.*800C>T Single submitter renal hypomagnesemia 5 with ocular involvement
- c.*867C>G Single submitter renal hypomagnesemia 5 with ocular involvement
- p.Ala121Thr Single submitter Inborn genetic diseases ⚠
- p.Ala129Pro Single submitter renal hypomagnesemia 5 with ocular involvement ⚠
- p.Ala136Val Single submitter Inborn genetic diseases ⚠
- p.Ala14Asp Single submitter ⚠
- p.Ala175Val Single submitter Inborn genetic diseases ⚠
- p.Ala206Val Single submitter renal hypomagnesemia 5 with ocular involvement ⚠
- p.Ala207Thr Single submitter ⚠
- p.Ala36Ser Single submitter renal hypomagnesemia 5 with ocular involvement ⚠
- p.Gln61Pro Single submitter Inborn genetic diseases ⚠
- p.Glu147Lys Single submitter renal hypomagnesemia 5 with ocular involvement ⚠
- p.Gly168Val Single submitter renal hypomagnesemia 5 with ocular involvement ⚠
- p.Gly17fs Single submitter renal hypomagnesemia 5 with ocular involvement
- p.Gly220Val Single submitter renal hypomagnesemia 5 with ocular involvement ⚠
- p.Gly37Ser Single submitter Inborn genetic diseases ⚠
- p.Gly60Arg Single submitter Inborn genetic diseases ⚠
- p.Gly75Ala Single submitter Inborn genetic diseases ⚠
- p.Ile113Thr Single submitter ⚠
- p.Ile113Val Single submitter renal hypomagnesemia 5 with ocular involvement ⚠
- p.Ile21Thr Single submitter Inborn genetic diseases ⚠
- p.Leu134Phe Single submitter renal hypomagnesemia 5 with ocular involvement ⚠
- p.Lys219Glu Single submitter Inborn genetic diseases ⚠
- p.Lys31Arg Single submitter Inborn genetic diseases ⚠
- p.Met95Leu Single submitter Inborn genetic diseases ⚠
- p.Met95Val Single submitter ⚠
- p.Pro187Ser Single submitter Inborn genetic diseases ⚠
- p.Pro192Arg Single submitter Inborn genetic diseases ⚠
- p.Pro221Leu Single submitter Inborn genetic diseases ⚠
- p.Pro28Thr Single submitter Inborn genetic diseases ⚠
- p.Ser152Asn Single submitter renal hypomagnesemia 5 with ocular involvement ⚠
- p.Ser53Thr Single submitter Inborn genetic diseases ⚠
- p.Ser56= Single submitter renal hypomagnesemia 5 with ocular involvement
- p.Ser58Ile Single submitter renal hypomagnesemia 5 with ocular involvement ⚠
- p.Thr145Ala Single submitter Inborn genetic diseases ⚠
- p.Thr25Ile Single submitter ⚠
- p.Thr42Ala Single submitter renal hypomagnesemia 5 with ocular involvement ⚠
- p.Tyr11His Single submitter renal hypomagnesemia 5 with ocular involvement ⚠
- p.Tyr47Cys Single submitter renal hypomagnesemia 5 with ocular involvement ⚠
- p.Val137Phe Single submitter ⚠
- p.Val176Leu Single submitter renal hypomagnesemia 5 with ocular involvement ⚠
- p.Val44Leu Single submitter ⚠
- p.Val86Ala Single submitter ⚠
- p.Val88Met Single submitter Inborn genetic diseases ⚠
- p.Val93Leu Single submitter renal hypomagnesemia 5 with ocular involvement ⚠
- c.626+15_626+17delinsTGT No assertion criteria
- p.Ala43Val No assertion criteria ⚠
- p.Gly101Ser No assertion criteria ⚠