PRDM12 — 278 ClinVar variants

All ClinVar germline PRDM12 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 115 flagged for review →

10 Pathogenic · 5 Likely pathogenic · 9 Conflicting · 18 Benign · 6 Benign/Likely benign · 97 Likely benign · 133 Uncertain significance

Full PRDM12 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 115

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.

Predictors agree, ClinVar conflicts 2

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

Predictors lean, ClinVar uncertain 88

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

Predictors split 24

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

All PRDM12 variants

Pathogenic 10

  • c.224-1G>A Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Glu172Asp Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Glu172Ter Single submitter Inborn genetic diseases
  • p.Ile189fs Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Met262Arg Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Pro194fs Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Val44fs Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • c.1041CGC[(15_? No assertion criteria congenital insensitivity to pain-hypohidrosis syndrome
  • p.Asp31Tyr No assertion criteria congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.His289Leu No assertion criteria congenital insensitivity to pain-hypohidrosis syndrome

Likely pathogenic 5

Conflicting classifications of pathogenicity 9

  • p.341HA[3] Single submitter Inborn genetic diseases
  • p.Ala356_Ala359dup Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Ala357_Ala359dup Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Ala359del Single submitter Inborn genetic diseases
  • p.Arg168His Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Arg263His Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Cys248Gly Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Gly203Arg Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Ser327Thr Single submitter Inborn genetic diseases ⚠

Benign 18

Benign/Likely benign 6

  • c.570+1GT[7] Multiple submitters congenital insensitivity to pain-hypohidrosis syndrome
  • p.Ala354_Ala359del Multiple submitters congenital insensitivity to pain-hypohidrosis syndrome
  • p.Ala355_Ala359del Multiple submitters congenital insensitivity to pain-hypohidrosis syndrome
  • p.Ala358_Ala359del Multiple submitters congenital insensitivity to pain-hypohidrosis syndrome
  • p.Ala358_Ala359dup Multiple submitters congenital insensitivity to pain-hypohidrosis syndrome
  • p.Thr285= Multiple submitters congenital insensitivity to pain-hypohidrosis syndrome

Likely benign 97

  • c.224-37C>T Multiple submitters
  • p.Ala237= Multiple submitters Inborn genetic diseases
  • p.Ala332Glu Multiple submitters Inborn genetic diseases
  • p.Ala355= Multiple submitters congenital insensitivity to pain-hypohidrosis syndrome
  • p.Ala356_Ala359del Multiple submitters Inborn genetic diseases
  • p.Glu142= Multiple submitters congenital insensitivity to pain-hypohidrosis syndrome
  • p.Ile150= Multiple submitters congenital insensitivity to pain-hypohidrosis syndrome
  • p.Ile180= Multiple submitters congenital insensitivity to pain-hypohidrosis syndrome
  • p.Ser73= Multiple submitters congenital insensitivity to pain-hypohidrosis syndrome
  • p.Tyr202= Multiple submitters congenital insensitivity to pain-hypohidrosis syndrome
  • c.223+170C>T Single submitter
  • c.223+18A>G Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • c.223+9A>G Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • c.224-14C>T Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • c.224-15G>T Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • c.224-254C>T Single submitter
  • c.415-12A>G Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • c.415-13C>A Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • c.415-15T>G Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • c.415-176T>G Single submitter
  • c.415-200C>A Single submitter
  • c.415-20C>T Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • c.415-279C>G Single submitter
  • c.570+17G>T Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • c.570+1GT[10] Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • c.570+1GT[3] Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • c.571-11C>T Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • c.571-14C>T Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • c.571-15C>T Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • c.571-36G>A Single submitter
  • c.682+103G>A Single submitter
  • c.682+10C>A Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • c.682+10C>T Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • c.682+14A>G Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • c.682+18G>A Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • c.682+8T>A Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • c.682+8T>C Single submitter
  • c.683-18G>C Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • c.683-294T>C Single submitter
  • c.*51C>T Single submitter
  • p.Ala19= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Ala23= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Ala25= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Ala329= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Ala332= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Ala344= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Ala353fs Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Ala354= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Ala359= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Ala69= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Arg315= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Asn169= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Asn257= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Asp221= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Asp31= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Cys245= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Cys248= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Gln331= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Gln48= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Glu176= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Glu51= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Glu66= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Gly16= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Gly46= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.His157= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.His265= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.His56= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Ile189= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Ile192= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Leu198= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Leu218= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Leu24= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Leu286= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Leu337= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Leu362= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Pro213= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Pro232= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Pro270= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Pro325= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Pro335= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Pro338= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Pro340= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Pro345= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Pro59= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Ser283= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Ser334= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Ser71= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Thr145= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Thr294= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Thr328Ala Single submitter Inborn genetic diseases
  • p.Thr61= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Thr64= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Tyr299= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Val139= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Val246= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Val27= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Val44= Single submitter congenital insensitivity to pain-hypohidrosis syndrome

Uncertain significance 133

  • p.Ala332Val Multiple submitters Inborn genetic diseases ⚠
  • p.Ala339_Pro340insHisSerProAlaLeuProAla Multiple submitters congenital insensitivity to pain-hypohidrosis syndrome
  • p.Ala348_Ala349insThr Multiple submitters congenital insensitivity to pain-hypohidrosis syndrome
  • p.Ala353_Ala359del Multiple submitters congenital insensitivity to pain-hypohidrosis syndrome
  • p.Ala355_Ala359dup Multiple submitters hereditary sensory and autonomic neuropathy
  • p.Arg147Cys Multiple submitters Inborn genetic diseases
  • p.Arg147His Multiple submitters Inborn genetic diseases ⚠
  • p.Arg158Trp Multiple submitters Inborn genetic diseases ⚠
  • p.Asn134Ser Multiple submitters Inborn genetic diseases ⚠
  • p.Asn141Ser Multiple submitters congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Asn207Ser Multiple submitters congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Asn277Lys Multiple submitters congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Asn43Asp Multiple submitters Inborn genetic diseases ⚠
  • p.Asn43Ser Multiple submitters congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Glu142Gly Multiple submitters Inborn genetic diseases ⚠
  • p.Glu170Lys Multiple submitters congenital insensitivity to pain-hypohidrosis syndrome
  • p.Glu228Gln Multiple submitters Inborn genetic diseases ⚠
  • p.Gly16Arg Multiple submitters Inborn genetic diseases ⚠
  • p.Gly181Ser Multiple submitters Inborn genetic diseases ⚠
  • p.His333Tyr Multiple submitters Inborn genetic diseases ⚠
  • p.His341Pro Multiple submitters Inborn genetic diseases ⚠
  • p.His343Pro Multiple submitters Inborn genetic diseases ⚠
  • p.Ile180Val Multiple submitters Inborn genetic diseases ⚠
  • p.Leu347Pro Multiple submitters congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Leu6Ile Multiple submitters congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Met191Thr Multiple submitters Inborn genetic diseases ⚠
  • p.Met1Lys Multiple submitters Inborn genetic diseases
  • p.Met2Ile Multiple submitters Inborn genetic diseases
  • p.Pro345His Multiple submitters Inborn genetic diseases ⚠
  • p.Ser183Gly Multiple submitters Inborn genetic diseases ⚠
  • p.Ser58Thr Multiple submitters congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Ala10Val Single submitter ⚠
  • p.Ala167Thr Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Ala188Thr Single submitter Inborn genetic diseases ⚠
  • p.Ala329fs Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Ala329Val Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Ala336Val Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Ala346Gly Single submitter Inborn genetic diseases ⚠
  • p.Ala348Thr Single submitter Inborn genetic diseases ⚠
  • p.Ala349_Ala350insAspAlaAla Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Ala350Thr Single submitter Inborn genetic diseases ⚠
  • p.Ala353_Ala359dup Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Ala356Val Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Ala359_His360insAla Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Ala359_His360insSer Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Ala359Val Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Arg158Gln Single submitter Inborn genetic diseases ⚠
  • p.Arg259Gly Single submitter ⚠
  • p.Arg263Ser Single submitter ⚠
  • p.Arg279Gly Single submitter Inborn genetic diseases ⚠
  • p.Arg297Leu Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Arg322Gln Single submitter Inborn genetic diseases ⚠
  • p.Arg40Cys Single submitter Inborn genetic diseases ⚠
  • p.Asn174Lys Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Asp221Ala Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Cys166Arg Single submitter Inborn genetic diseases ⚠
  • p.Cys273Ter Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Gln305Leu Single submitter Inborn genetic diseases ⚠
  • p.Gln318Leu Single submitter Inborn genetic diseases ⚠
  • p.Gln331_Leu337dup Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Gln331Arg Single submitter ⚠
  • p.Glu172Gly Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Glu219Lys Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Glu26Asp Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Glu75Lys Single submitter Inborn genetic diseases ⚠
  • p.Gly144Ala Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Gly144Ser Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Gly16Ala Single submitter Inborn genetic diseases ⚠
  • p.Gly211Glu Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Gly214Ser Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Gly214Val Single submitter Inborn genetic diseases
  • p.Gly217Arg Single submitter Inborn genetic diseases ⚠
  • p.Gly21Glu Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Gly295Asp Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Gly3Val Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.His227= Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.His265Gln Single submitter ⚠
  • p.His265Pro Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.His289Arg Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.His317Leu Single submitter Inborn genetic diseases ⚠
  • p.His333_Ala339dup Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.His333Gln Single submitter Inborn genetic diseases ⚠
  • p.His341Gln Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Ile189Thr Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Leu11Met Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Leu330Pro Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Leu337Gln Single submitter Inborn genetic diseases ⚠
  • p.Leu347del Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Leu347Val Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Leu362Gln Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Leu6Phe Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Lys14Gln Single submitter Inborn genetic diseases ⚠
  • p.Lys223Gln Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Lys319Glu Single submitter Inborn genetic diseases ⚠
  • p.Lys319Met Single submitter Inborn genetic diseases ⚠
  • p.Lys53Arg Single submitter ⚠
  • p.Lys53Asn Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Lys60Asn Single submitter Inborn genetic diseases ⚠
  • p.Met1Thr Single submitter Inborn genetic diseases
  • p.Met243Ile Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Met262Ile Single submitter Inborn genetic diseases ⚠
  • p.Met365Ile Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Met365Val Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Phe36Ser Single submitter Inborn genetic diseases ⚠
  • p.Pro20Arg Single submitter Inborn genetic diseases ⚠
  • p.Pro20Gln Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Pro20Ser Single submitter Inborn genetic diseases ⚠
  • p.Pro270Ser Single submitter ⚠
  • p.Pro325Leu Single submitter Inborn genetic diseases ⚠
  • p.Pro326Ala Single submitter Inborn genetic diseases ⚠
  • p.Pro335Thr Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Pro338His Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Pro338Ser Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Pro345_Ala346dup Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Pro345_Ala348dup Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Pro345Ala Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Pro345Leu Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Pro7Leu Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Ser159Asn Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Ser256_Arg263dup Single submitter congenital insensitivity to pain-hypohidrosis syndrome
  • p.Ser256Gly Single submitter Inborn genetic diseases ⚠
  • p.Ser320Gly Single submitter Inborn genetic diseases ⚠
  • p.Ser327Gly Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Ser334Leu Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Ser54Asn Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Thr145Met Single submitter Inborn genetic diseases ⚠
  • p.Thr145Pro Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Thr328Ile Single submitter Inborn genetic diseases ⚠
  • p.Thr328Pro Single submitter Inborn genetic diseases ⚠
  • p.Thr328Ser Single submitter Inborn genetic diseases ⚠
  • p.Thr61Ile Single submitter congenital insensitivity to pain-hypohidrosis syndrome ⚠
  • p.Tyr186Cys Single submitter ⚠
  • p.Val246Leu Single submitter ⚠