CLCN5 — 577 ClinVar variants

All ClinVar germline CLCN5 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 206 flagged for review →

74 Pathogenic · 7 Pathogenic/Likely pathogenic · 70 Likely pathogenic · 28 Conflicting · 31 Benign · 15 Benign/Likely benign · 91 Likely benign · 261 Uncertain significance

Full CLCN5 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 206

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 agree, ClinVar conflicts 15

ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.

Predicted LoF vs a conflicting call 1

ClinVar submitters conflict, and it's a predicted loss-of-function change in a gene where LoF causes disease — flagged for review, not resolved (verify NMD-escape for C-terminal truncations). Non-missense.

Predictors lean, ClinVar uncertain 136

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.

Predictors split 54

The independent predictors disagree with each other — read with care.

All CLCN5 variants

Pathogenic 74

Pathogenic/Likely pathogenic 7

  • c.1014+1G>A Multiple submitters nephrolithiasis, X-linked recessive, with renal failure
  • c.933+1G>A Multiple submitters Dent disease type 1
  • p.Arg104Ter Multiple submitters proteinuria, low molecular weight, with hypercalciuria and nephrocalcinosis
  • p.Arg586Trp Multiple submitters nephrolithiasis, X-linked recessive, with renal failure
  • p.Arg98Ter Multiple submitters CLCN5-related disorder
  • p.Tyr342Cys Multiple submitters CLCN5-related disorder
  • p.Tyr425Ter Multiple submitters hypophosphatemic rickets, X-linked recessive

Likely pathogenic 70

  • c.604-1G>C Multiple submitters Dent disease type 1
  • p.Cys291Arg Multiple submitters hypophosphatemic rickets, X-linked recessive
  • p.Gln421Ter Multiple submitters CLCN5-related disorder
  • p.Gln545Ter Multiple submitters proteinuria, low molecular weight, with hypercalciuria and nephrocalcinosis
  • p.Ser615Asn Multiple submitters CLCN5-related disorder
  • p.Tyr687Ter Multiple submitters Dent disease type 1
  • c.1015-1G>A Single submitter
  • c.1015-2A>T Single submitter CLCN5-related disorder
  • c.1558-2A>G Single submitter Dent disease
  • c.1744+1G>C Single submitter hypophosphatemic rickets, X-linked recessive
  • c.1745-1G>A Single submitter
  • c.2143_2143+10del Single submitter
  • c.2144-2A>G Single submitter Dent disease type 1
  • c.2361-1G>C Single submitter CLCN5-related disorder
  • c.315+1G>A Single submitter
  • c.416-1G>A Single submitter hypophosphatemic rickets, X-linked recessive
  • c.416-1G>C Single submitter
  • p.Ala116_Leu117insTer Single submitter hypophosphatemic rickets, X-linked recessive
  • p.Ala203fs Single submitter CLCN5-related disorder
  • p.Ala535Ter Single submitter hypophosphatemic rickets, X-linked recessive
  • p.Arg624fs Single submitter Dent disease type 1
  • p.Arg659fs Single submitter hypophosphatemic rickets, X-linked recessive
  • p.Asp762fs Single submitter
  • p.Glu105= Single submitter Dent disease type 1
  • p.Glu169Ter Single submitter Dent disease type 1
  • p.Glu597Ala Single submitter hypophosphatemic rickets, X-linked recessive
  • p.Glu597Ter Single submitter Dent disease type 1
  • p.Glu645Ter Single submitter CLCN5-related disorder
  • p.Gly127Arg Single submitter Dent disease type 1
  • p.Gly249Val Single submitter Dent disease type 1
  • p.Gly483fs Single submitter proteinuria, low molecular weight, with hypercalciuria and nephrocalcinosis
  • p.Gly517_Met518insTer Single submitter Hyperkalemia
  • p.Gly532Asp Single submitter hypophosphatemic rickets, X-linked recessive
  • p.Gly576Arg Single submitter
  • p.Gly582Val Single submitter CLCN5-related disorder
  • p.Gly703Asp Single submitter Dent disease type 1
  • p.Leu333Phe Single submitter proteinuria, low molecular weight, with hypercalciuria and nephrocalcinosis
  • p.Leu386_Phe387insTer Single submitter CLCN5-related disorder
  • p.Leu507fs Single submitter Dent disease type 1
  • p.Leu539Arg Single submitter hypophosphatemic rickets, X-linked recessive
  • p.Leu591Phe Single submitter CLCN5-related disorder
  • p.Leu763fs Single submitter CLCN5-related disorder
  • p.Lys111fs Single submitter Dent disease type 1
  • p.Lys258Ter Single submitter hypophosphatemic rickets, X-linked recessive
  • p.Lys301Arg Single submitter CLCN5-related disorder
  • p.Lys301Ile Single submitter Dent disease type 1
  • p.Phe380fs Single submitter hypophosphatemic rickets, X-linked recessive
  • p.Phe646fs Single submitter CLCN5-related disorder
  • p.Pro527fs Single submitter Dent disease type 1
  • p.Pro607Arg Single submitter hypophosphatemic rickets, X-linked recessive
  • p.Ser335Asn Single submitter CLCN5-related disorder
  • p.Ser351Ter Single submitter hypophosphatemic rickets, X-linked recessive
  • p.Ser522fs Single submitter hypophosphatemic rickets, X-linked recessive
  • p.Ser528fs Single submitter CLCN5-related disorder
  • p.Thr599Ile Single submitter
  • p.Thr764fs Single submitter hypophosphatemic rickets, X-linked recessive
  • p.Trp189Ter Single submitter hypophosphatemic rickets, X-linked recessive
  • p.Trp259Ter Single submitter Dent disease type 1
  • p.Trp553Ter Single submitter hypophosphatemic rickets, X-linked recessive
  • p.Trp559Ter Single submitter Dent disease type 1
  • p.Tyr495Ter Single submitter hypophosphatemic rickets, X-linked recessive
  • p.Tyr548Ter Single submitter CLCN5-related disorder
  • p.Val589fs Single submitter Dent disease type 1
  • p.Val93fs Single submitter hypophosphatemic rickets, X-linked recessive
  • c.2360+2T>G No assertion criteria CLCN5-related disorder
  • c.416-2A>G No assertion criteria CLCN5-related disorder
  • p.Ala577fs No assertion criteria Dent disease type 1
  • p.Leu706Phe No assertion criteria
  • p.Trp128Cys No assertion criteria Dent disease type 1
  • p.Trp192Arg No assertion criteria Hypophosphataemia, X-linked

Conflicting classifications of pathogenicity 28

Benign 31

Benign/Likely benign 15

  • c.2361-18A>G Multiple submitters Dent disease type 1
  • c.315+12G>A Multiple submitters nephrolithiasis, X-linked recessive, with renal failure
  • c.316-17T>G Multiple submitters Bethlem myopathy 1A
  • c.727-5T>C Multiple submitters
  • p.Arg408His Multiple submitters hypophosphatemic rickets, X-linked recessive
  • p.Arg415Gln Multiple submitters ⚠
  • p.Glu474= Multiple submitters hypophosphatemic rickets, X-linked recessive
  • p.His150= Multiple submitters
  • p.Met212Ile Multiple submitters Dent disease type 1
  • p.Ser273= Multiple submitters Dent disease type 1
  • p.Ser496= Multiple submitters Dent disease type 1
  • p.Thr419= Multiple submitters hypophosphatemic rickets, X-linked recessive
  • p.Thr554= Multiple submitters
  • p.Thr650= Multiple submitters
  • p.Thr669= Multiple submitters

Likely benign 91

Uncertain significance 261