SLC34A3 — 859 ClinVar variants

All ClinVar germline SLC34A3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 336 flagged for review →

31 Pathogenic · 17 Pathogenic/Likely pathogenic · 44 Likely pathogenic · 60 Conflicting · 18 Benign · 26 Benign/Likely benign · 285 Likely benign · 378 Uncertain significance

Full SLC34A3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 336

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 2

ClinVar calls these pathogenic, but the computational predictors lean tolerated — the highest-value review flag.

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 236

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 236

Predictors split 79

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

All SLC34A3 variants

Pathogenic 31

  • p.Gly337fs Multiple submitters hereditary hypophosphatemic rickets with hypercalciuria
  • p.Gly457Ser Multiple submitters hereditary hypophosphatemic rickets with hypercalciuria
  • p.Ile238fs Multiple submitters Inborn genetic diseases
  • p.Leu246fs Multiple submitters hereditary hypophosphatemic rickets with hypercalciuria
  • c.1093+68_1106del Single submitter
  • c.1336-11_1336-1del Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • c.926-1G>A Single submitter
  • c.926-2A>G Single submitter
  • p.Arg547fs Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • p.Gln281Ter Single submitter
  • p.Gln390Ter Single submitter
  • p.Gln49Ter Single submitter
  • p.Gln98Ter Single submitter
  • p.Gly315fs Single submitter
  • p.Gly406Val Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • p.Gly519fs Single submitter
  • p.Gly71fs Single submitter
  • p.Ile529fs Single submitter
  • p.Leu416fs Single submitter
  • p.Leu493fs Single submitter
  • p.Phe368fs Single submitter Inborn genetic diseases
  • p.Pro245fs Single submitter
  • p.Pro303fs Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • p.Pro48fs Single submitter
  • p.Ser192Trp Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • p.Trp372Ter Single submitter
  • p.Trp45Ter Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • p.Trp541Ter Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • c.1093+41_1094-15del No assertion criteria hereditary hypophosphatemic rickets with hypercalciuria
  • p.Cys77fs No assertion criteria hereditary hypophosphatemic rickets with hypercalciuria
  • p.Pro520fs No assertion criteria hereditary hypophosphatemic rickets with hypercalciuria

Pathogenic/Likely pathogenic 17

  • c.1093+1G>C Multiple submitters SLC34A3-related disorder
  • c.1093+2T>C Multiple submitters hereditary hypophosphatemic rickets with hypercalciuria
  • c.1335+2T>A Multiple submitters hereditary hypophosphatemic rickets with hypercalciuria
  • c.448+1G>A Multiple submitters hereditary hypophosphatemic rickets with hypercalciuria
  • c.448+2T>C Multiple submitters hereditary hypophosphatemic rickets with hypercalciuria
  • c.925+20_926-48del Multiple submitters hereditary hypophosphatemic rickets with hypercalciuria
  • p.Ala413Glu Multiple submitters hereditary hypophosphatemic rickets with hypercalciuria
  • p.Arg468Trp Multiple submitters hereditary hypophosphatemic rickets with hypercalciuria
  • p.Gly196Arg Multiple submitters SLC34A3-related disorder ⚠
  • p.Leu224fs Multiple submitters hereditary hypophosphatemic rickets with hypercalciuria
  • p.Leu417fs Multiple submitters hereditary hypophosphatemic rickets with hypercalciuria
  • p.Leu521fs Multiple submitters hereditary hypophosphatemic rickets with hypercalciuria
  • p.Met1Ile Multiple submitters hereditary hypophosphatemic rickets with hypercalciuria
  • p.Met1Thr Multiple submitters hereditary hypophosphatemic rickets with hypercalciuria
  • p.Ser192Leu Multiple submitters Hypophosphataemia or rickets
  • p.Tyr414Ter Multiple submitters hereditary hypophosphatemic rickets with hypercalciuria
  • p.Val349fs Multiple submitters hereditary hypophosphatemic rickets with hypercalciuria

Likely pathogenic 44

  • c.1094-63_1115del Multiple submitters hereditary hypophosphatemic rickets with hypercalciuria
  • c.176-1G>A Multiple submitters hereditary hypophosphatemic rickets with hypercalciuria
  • c.305-1G>C Multiple submitters SLC34A3-related disorder
  • c.449-1G>C Multiple submitters hereditary hypophosphatemic rickets with hypercalciuria
  • c.846+1G>A Multiple submitters hereditary hypophosphatemic rickets with hypercalciuria
  • c.1093_1093+9del Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • c.1094-2A>G Single submitter
  • c.1094-44_1134del Single submitter
  • c.1210+2T>C Single submitter
  • c.1211-1G>A Single submitter
  • c.1335+1G>C Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • c.1336-1G>A Single submitter
  • c.1336-1G>T Single submitter
  • c.1336-2A>C Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • c.175+1G>A Single submitter
  • c.175+1G>T Single submitter
  • c.449-18_456del Single submitter
  • c.561-1G>A Single submitter
  • c.756+1G>C Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • c.757-1G>A Single submitter
  • c.85+1G>A Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • c.926-1G>C Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • p.Arg187Met Single submitter SLC34A3-related disorder
  • p.Arg61fs Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • p.Cys276Ter Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • p.Cys289Ter Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • p.Gln234Ter Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • p.Gln535Ter Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • p.Gly404Arg Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • p.Gly419Asp Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • p.Leu370= Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • p.Leu441fs Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • p.Leu501fs Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • p.Leu66fs Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • p.Pro369Leu Single submitter hereditary hypophosphatemic rickets with hypercalciuria ⚠
  • p.Trp200Ter Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • p.Trp461Ter Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • p.Trp551Ter Single submitter
  • p.Tyr376Ter Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • p.Val487fs Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • p.Ile197Val No assertion criteria Hypercalciuria ⚠
  • p.Ser171Arg No assertion criteria hereditary hypophosphatemic rickets with hypercalciuria
  • p.Thr425Ile No assertion criteria hereditary hypophosphatemic rickets with hypercalciuria
  • p.Tyr462Ter No assertion criteria hereditary hypophosphatemic rickets with hypercalciuria

Conflicting classifications of pathogenicity 60

  • c.304+2T>C Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • c.305-7G>A Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • c.448+5G>A Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • c.449-14C>A Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • c.449-3C>T Single submitter
  • c.449-9C>G Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • c.449-9dup Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • c.560+27_561-38del Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • c.925+32C>G Single submitter
  • c.-39-1G>A Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • p.Ala233Val Single submitter Inborn genetic diseases ⚠
  • p.Ala329= Single submitter
  • p.Ala364= Single submitter
  • p.Ala383= Single submitter
  • p.Ala388= Single submitter
  • p.Ala488= Single submitter
  • p.Ala70= Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • p.Arg154Trp Single submitter Inborn genetic diseases ⚠
  • p.Arg187= Single submitter Inborn genetic diseases
  • p.Arg353Leu Single submitter SLC34A3-related disorder ⚠
  • p.Arg412Trp Single submitter hereditary hypophosphatemic rickets with hypercalciuria ⚠
  • p.Arg485Cys Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • p.Arg485His Single submitter hereditary hypophosphatemic rickets with hypercalciuria ⚠
  • p.Arg568Cys Single submitter Inborn genetic diseases ⚠
  • p.Arg65_Gly71del Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • p.Asn265= Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • p.Gln252= Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • p.Gly125= Single submitter
  • p.Gly166Ser Single submitter hereditary hypophosphatemic rickets with hypercalciuria ⚠
  • p.Gly264Ser Single submitter hereditary hypophosphatemic rickets with hypercalciuria ⚠
  • p.Gly293Ser Single submitter Inborn genetic diseases ⚠
  • p.Gly315= Single submitter
  • p.Gly374Ser Single submitter Inborn genetic diseases ⚠
  • p.Gly423Asp Single submitter hereditary hypophosphatemic rickets with hypercalciuria ⚠
  • p.Gly495Ala Single submitter Inborn genetic diseases ⚠
  • p.Gly81Asp Single submitter Inborn genetic diseases ⚠
  • p.Ile326= Single submitter
  • p.Ile529Phe Single submitter hereditary hypophosphatemic rickets with hypercalciuria ⚠
  • p.Leu215Pro Single submitter Inborn genetic diseases ⚠
  • p.Leu307Met Single submitter hereditary hypophosphatemic rickets with hypercalciuria ⚠
  • p.Leu527del Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • p.Met403Arg Single submitter hereditary hypophosphatemic rickets with hypercalciuria ⚠
  • p.Met512Thr Single submitter hereditary hypophosphatemic rickets with hypercalciuria ⚠
  • p.Phe453del Single submitter SLC34A3-related disorder
  • p.Pro282= Single submitter SLC34A3-related disorder
  • p.Pro294= Single submitter
  • p.Ser138Phe Single submitter SLC34A3-related disorder ⚠
  • p.Ser255= Single submitter
  • p.Ser435fs Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • p.Thr137Met Single submitter hereditary hypophosphatemic rickets with hypercalciuria ⚠
  • p.Thr213Met Single submitter Inborn genetic diseases ⚠
  • p.Thr279= Single submitter
  • p.Thr316= Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • p.Trp555Ter Single submitter hereditary hypophosphatemic rickets with hypercalciuria
  • p.Tyr491= Single submitter
  • p.Val153Ala Single submitter hereditary hypophosphatemic rickets with hypercalciuria ⚠
  • p.Val165Ile Single submitter ⚠
  • p.Val358= Single submitter SLC34A3-related disorder
  • p.Val399Ile Single submitter Inborn genetic diseases ⚠
  • p.Val92Ile Single submitter Inborn genetic diseases ⚠

Benign 18

Benign/Likely benign 26

  • c.1093+19G>A Multiple submitters hereditary hypophosphatemic rickets with hypercalciuria
  • c.1093+8C>T Multiple submitters hereditary hypophosphatemic rickets with hypercalciuria
  • c.1210+17G>A Multiple submitters hereditary hypophosphatemic rickets with hypercalciuria
  • c.1336-8G>A Multiple submitters
  • c.175+123C>T Multiple submitters
  • c.304+20C>T Multiple submitters hereditary hypophosphatemic rickets with hypercalciuria
  • c.449-9del Multiple submitters
  • c.756+21dup Multiple submitters
  • p.Ala227Thr Multiple submitters
  • p.Ala314= Multiple submitters hereditary hypophosphatemic rickets with hypercalciuria
  • p.Ala515= Multiple submitters
  • p.Arg310His Multiple submitters Inborn genetic diseases
  • p.Asp107= Multiple submitters
  • p.Asp237Asn Multiple submitters hereditary hypophosphatemic rickets with hypercalciuria
  • p.Asp91= Multiple submitters hereditary hypophosphatemic rickets with hypercalciuria
  • p.Cys276= Multiple submitters hereditary hypophosphatemic rickets with hypercalciuria
  • p.Gly180Ala Multiple submitters hereditary hypophosphatemic rickets with hypercalciuria
  • p.Gly337Ser Multiple submitters
  • p.Ile159= Multiple submitters
  • p.Leu209= Multiple submitters hereditary hypophosphatemic rickets with hypercalciuria
  • p.Leu494= Multiple submitters hereditary hypophosphatemic rickets with hypercalciuria
  • p.Phe292= Multiple submitters hereditary hypophosphatemic rickets with hypercalciuria
  • p.Phe504= Multiple submitters hereditary hypophosphatemic rickets with hypercalciuria
  • p.Ser260Asn Multiple submitters
  • p.Thr279Met Multiple submitters
  • p.Val357= Multiple submitters hereditary hypophosphatemic rickets with hypercalciuria

Likely benign 285

Uncertain significance 378

Showing the top 300 by review status; the full set is in the sitemap.