Sugi Variant

Sugi Variant/SLC34A1

SLC34A1 — 585 ClinVar variants

All ClinVar germline SLC34A1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 254 flagged for review →

22 Pathogenic · 8 Pathogenic/Likely pathogenic · 26 Likely pathogenic · 44 Conflicting · 21 Benign · 13 Benign/Likely benign · 167 Likely benign · 284 Uncertain significance

Full SLC34A1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 254

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 19

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

Predictors lean, ClinVar uncertain 190

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification. · showing the 150 best-reviewed of 190

Predictors split 45

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

All SLC34A1 variants

Pathogenic 22

Pathogenic/Likely pathogenic 8

  • c.1006+1G>A Multiple submitters hypercalcemia, infantile, 2
  • p.Arg249Ter Multiple submitters hypercalcemia, infantile, 2
  • p.Arg25Ter Multiple submitters Fanconi renotubular syndrome 2
  • p.Cys64fs Multiple submitters hypercalcemia, infantile, 2
  • p.Gly153Val Multiple submitters hypercalcemia, infantile, 2
  • p.Ser176fs Multiple submitters hypercalcemia, infantile, 2
  • p.Val152_Val160dup Multiple submitters hypercalcemia, infantile, 2
  • p.Val231fs Multiple submitters Fanconi renotubular syndrome 2

Likely pathogenic 26

Conflicting classifications of pathogenicity 44

  • c.1007-7C>G Single submitter hypophosphatemic nephrolithiasis/osteoporosis 1
  • c.110-6C>T Single submitter hypophosphatemic nephrolithiasis/osteoporosis 1
  • c.1175-13G>A Single submitter Fanconi renotubular syndrome 2
  • c.1175-3C>A Single submitter hypercalcemia, infantile, 2
  • c.1416+3G>A Single submitter
  • c.1416+5G>A Single submitter hypophosphatemic nephrolithiasis/osteoporosis 1
  • c.532+2T>C Single submitter hypercalcemia, infantile, 2
  • c.644+14G>T Single submitter hypophosphatemic nephrolithiasis/osteoporosis 1
  • c.644+15G>A Single submitter Fanconi renotubular syndrome 2
  • c.937-2A>C Single submitter nephrolithiasis
  • c.937-8T>A Single submitter Fanconi renotubular syndrome 2
  • p.Ala133Val Single submitter hypophosphatemic nephrolithiasis/osteoporosis 1 ⚠
  • p.Arg19His Single submitter hypercalcemia, infantile, 2 ⚠
  • p.Arg215Gln Single submitter SLC34A1-related disorder ⚠
  • p.Arg25Gln Single submitter hypophosphatemic nephrolithiasis/osteoporosis 1 ⚠
  • p.Arg261His Single submitter hypophosphatemic nephrolithiasis/osteoporosis 1 ⚠
  • p.Arg495Cys Single submitter hypercalcemia, infantile, 2 ⚠
  • p.Arg512Cys Single submitter hypophosphatemic nephrolithiasis/osteoporosis 1 ⚠
  • p.Arg581His Single submitter Inborn genetic diseases ⚠
  • p.Asp265Glu Single submitter hypophosphatemic nephrolithiasis/osteoporosis 1 ⚠
  • p.Cys476fs Single submitter hypercalcemia, infantile, 2
  • p.Glu238Ala Single submitter hypercalcemia, infantile, 2 ⚠
  • p.Glu82Ter Single submitter hypercalcemia, infantile, 2
  • p.Gly194Arg Single submitter hypercalcemia, infantile, 2 ⚠
  • p.Gly450Ser Single submitter Fanconi renotubular syndrome 2 ⚠
  • p.Gly9Trp Single submitter hypophosphatemic nephrolithiasis/osteoporosis 1 ⚠
  • p.Ile154_Val160dup Single submitter Fanconi renotubular syndrome 2
  • p.Leu155Pro Single submitter SLC34A1-related disorder ⚠
  • p.Leu179= Single submitter Fanconi renotubular syndrome 2
  • p.Phe137del Single submitter hypercalcemia, infantile, 2
  • p.Pro146= Single submitter
  • p.Pro146Leu Single submitter Fanconi renotubular syndrome 2 ⚠
  • p.Pro490Leu Single submitter hypophosphatemic nephrolithiasis/osteoporosis 1 ⚠
  • p.Ser295Thr Single submitter Inborn genetic diseases ⚠
  • p.Ser483= Single submitter hypercalcemia, infantile, 2
  • p.Thr391Met Single submitter hypophosphatemic nephrolithiasis/osteoporosis 1 ⚠
  • p.Thr575Ile Single submitter hypercalcemia, infantile, 2 ⚠
  • p.Trp538Ter Single submitter hypercalcemia, infantile, 2
  • p.Tyr489Cys Single submitter hypercalcemia, infantile, 2 ⚠
  • p.Val115Ile Single submitter Inborn genetic diseases ⚠
  • p.Val171Ile Single submitter Fanconi renotubular syndrome 2 ⚠
  • p.Val202Met Single submitter Fanconi renotubular syndrome 2 ⚠
  • p.Val408Glu Single submitter hypercalcemia, infantile, 2 ⚠
  • p.Val91_Ala97del Single submitter Fetal anomalies with a likely genetic cause

Benign 21

Benign/Likely benign 13

  • c.388+10G>C Multiple submitters hypophosphatemic nephrolithiasis/osteoporosis 1
  • c.389-5C>T Multiple submitters hypophosphatemic nephrolithiasis/osteoporosis 1
  • c.*179G>A Multiple submitters hypophosphatemic nephrolithiasis/osteoporosis 1
  • c.*361T>C Multiple submitters hypophosphatemic nephrolithiasis/osteoporosis 1
  • p.Ala218Thr Multiple submitters hypophosphatemic nephrolithiasis/osteoporosis 1
  • p.Arg95His Multiple submitters hypophosphatemic nephrolithiasis/osteoporosis 1 ⚠
  • p.Gly545= Multiple submitters hypophosphatemic nephrolithiasis/osteoporosis 1
  • p.His568Tyr Multiple submitters hypophosphatemic nephrolithiasis/osteoporosis 1
  • p.Ile170= Multiple submitters hypophosphatemic nephrolithiasis/osteoporosis 1
  • p.Ile247= Multiple submitters Fanconi renotubular syndrome 2
  • p.Leu573= Multiple submitters hypophosphatemic nephrolithiasis/osteoporosis 1
  • p.Phe554= Multiple submitters
  • p.Val67Ile Multiple submitters

Likely benign 167

Uncertain significance 284