TMPRSS3 — 639 ClinVar variants

All ClinVar germline TMPRSS3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 140 flagged for review →

45 Pathogenic · 24 Pathogenic/Likely pathogenic · 47 Likely pathogenic · 49 Conflicting · 43 Benign · 11 Benign/Likely benign · 259 Likely benign · 161 Uncertain significance

Full TMPRSS3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 140

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 4

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

Predictors agree, ClinVar conflicts 22

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

Predictors lean, ClinVar uncertain 94

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

Predictors split 20

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

All TMPRSS3 variants

Pathogenic 45

Pathogenic/Likely pathogenic 24

  • c.323-6G>A Multiple submitters TMPRSS3-related disorder
  • p.Ala138Glu Multiple submitters TMPRSS3-related disorder
  • p.Ala306Thr Multiple submitters TMPRSS3-related disorder
  • p.Ala425Thr Multiple submitters TMPRSS3-related disorder
  • p.Arg106Cys Multiple submitters autosomal recessive nonsyndromic hearing loss 8 ⚠
  • p.Arg109Trp Multiple submitters TMPRSS3-related disorder
  • p.Arg16Ter Multiple submitters autosomal recessive nonsyndromic hearing loss 8
  • p.Asp334fs Multiple submitters autosomal recessive nonsyndromic hearing loss 8
  • p.Cys194fs Multiple submitters Rare genetic deafness
  • p.Cys406Arg Multiple submitters autosomal recessive nonsyndromic hearing loss 8
  • p.Glu104Lys Multiple submitters autosomal recessive nonsyndromic hearing loss 8
  • p.Gly243Arg Multiple submitters Rare genetic deafness
  • p.Gly401Arg Multiple submitters autosomal recessive nonsyndromic hearing loss 8
  • p.His70fs Multiple submitters TMPRSS3-related disorder
  • p.Lys134Ter Multiple submitters autosomal recessive nonsyndromic hearing loss 8
  • p.Met447Thr Multiple submitters Rare genetic deafness
  • p.Pro403Leu Multiple submitters autosomal recessive nonsyndromic hearing loss 8
  • p.Ser153Ter Multiple submitters TMPRSS3-related disorder
  • p.Ser215fs Multiple submitters autosomal recessive nonsyndromic hearing loss 8
  • p.Thr248Met Multiple submitters autosomal recessive nonsyndromic hearing loss 8 ⚠
  • p.Trp343Ter Multiple submitters autosomal recessive nonsyndromic hearing loss 8
  • p.Val116Met Multiple submitters TMPRSS3-related disorder ⚠
  • p.Val337fs Multiple submitters TMPRSS3-related disorder
  • c.783-1G>T No assertion criteria autosomal recessive nonsyndromic hearing loss 8

Likely pathogenic 47

  • c.1049-4G>A Multiple submitters autosomal recessive nonsyndromic hearing loss 8
  • c.206-2A>G Multiple submitters autosomal recessive nonsyndromic hearing loss 8
  • c.446+1G>T Multiple submitters autosomal recessive nonsyndromic hearing loss 8
  • c.573-1G>A Multiple submitters autosomal recessive nonsyndromic hearing loss 8
  • p.Ala306Val Multiple submitters autosomal recessive nonsyndromic hearing loss 8
  • p.Arg216His Multiple submitters Rare genetic deafness ⚠
  • p.Cys92Arg Multiple submitters autosomal recessive nonsyndromic hearing loss 8
  • p.Trp343Cys Multiple submitters autosomal recessive nonsyndromic hearing loss 8
  • c.1191+1G>A Single submitter
  • c.205+5G>C Single submitter autosomal recessive nonsyndromic hearing loss 8
  • c.447-1G>A Single submitter
  • c.447-1G>C Single submitter
  • c.616+1G>T Single submitter
  • c.616+2T>C Single submitter TMPRSS3-related disorder
  • c.95-2A>C Single submitter
  • c.952+1G>T Single submitter
  • c.953-1G>A Single submitter
  • c.953-2A>G Single submitter autosomal recessive nonsyndromic hearing loss 8
  • p.Ala306Asp Single submitter
  • p.Ala386Pro Single submitter
  • p.Arg435Leu Single submitter
  • p.Asp394Asn Single submitter ⚠
  • p.Asp399Val Single submitter autosomal recessive nonsyndromic hearing loss 8
  • p.Cys142Ser Single submitter autosomal recessive nonsyndromic hearing loss 8
  • p.Cys142Tyr Single submitter
  • p.Cys194Phe Single submitter Monogenic hearing loss
  • p.Cys385Arg Single submitter autosomal recessive nonsyndromic hearing loss 8
  • p.Cys424Ter Single submitter autosomal recessive nonsyndromic hearing loss 8
  • p.Glu104Gly Single submitter autosomal recessive nonsyndromic hearing loss 8
  • p.Gly146Ser Single submitter
  • p.Gly273Val Single submitter autosomal recessive nonsyndromic hearing loss 8
  • p.Gly342Glu Single submitter Rare genetic deafness
  • p.Gly401Trp Single submitter
  • p.Ile443Thr Single submitter autosomal recessive nonsyndromic hearing loss 8 ⚠
  • p.Leu63Arg Single submitter autosomal recessive nonsyndromic hearing loss 8
  • p.Pro322His Single submitter hearing loss disorder
  • p.Pro403Ala Single submitter
  • p.Pro403fs Single submitter autosomal recessive nonsyndromic hearing loss 8
  • p.Pro430Thr Single submitter
  • p.Ser14Ter Single submitter autosomal recessive nonsyndromic hearing loss 8
  • p.Ser341Ter Single submitter autosomal recessive nonsyndromic hearing loss 8
  • p.Thr340Arg Single submitter
  • p.Trp251Ter Single submitter autosomal recessive nonsyndromic hearing loss 8
  • p.Trp343Ser Single submitter
  • c.572+2T>G No assertion criteria autosomal recessive nonsyndromic hearing loss 8
  • p.Ala256Val No assertion criteria hearing loss, autosomal recessive
  • p.Asp100fs No assertion criteria autosomal recessive nonsyndromic hearing loss 8

Conflicting classifications of pathogenicity 49

  • c.1191+10C>T Single submitter autosomal recessive nonsyndromic hearing loss 8
  • c.1344+8C>T Single submitter autosomal recessive nonsyndromic hearing loss 8
  • c.1344+9G>A Single submitter autosomal recessive nonsyndromic hearing loss 8
  • c.573-8C>T Single submitter autosomal recessive nonsyndromic hearing loss 8
  • c.783-13C>A Single submitter
  • c.-131G>C Single submitter autosomal recessive nonsyndromic hearing loss 8
  • c.-36G>C Single submitter autosomal recessive nonsyndromic hearing loss 8
  • c.*53G>A Single submitter autosomal recessive nonsyndromic hearing loss 8
  • c.*815A>G Single submitter autosomal recessive nonsyndromic hearing loss 8
  • p.Ala138Thr Single submitter TMPRSS3-related disorder ⚠
  • p.Ala359= Single submitter autosomal recessive nonsyndromic hearing loss 8
  • p.Ala386Val Single submitter ⚠
  • p.Arg109Gln Single submitter TMPRSS3-related disorder ⚠
  • p.Arg166Leu Single submitter autosomal recessive nonsyndromic hearing loss 8 ⚠
  • p.Arg166Trp Single submitter autosomal recessive nonsyndromic hearing loss 8 ⚠
  • p.Arg435Cys Single submitter autosomal recessive nonsyndromic hearing loss 8 ⚠
  • p.Arg435His Single submitter Inborn genetic diseases
  • p.Arg80Cys Single submitter ⚠
  • p.Arg80His Single submitter autosomal recessive nonsyndromic hearing loss 8 ⚠
  • p.Asp348Asn Single submitter autosomal recessive nonsyndromic hearing loss 8 ⚠
  • p.Asp373= Single submitter autosomal recessive nonsyndromic hearing loss 8
  • p.Asp394His Single submitter autosomal recessive nonsyndromic hearing loss 8 ⚠
  • p.Asp399Glu Single submitter autosomal recessive nonsyndromic hearing loss 8 ⚠
  • p.Cys424= Single submitter autosomal recessive nonsyndromic hearing loss 8
  • p.Gln227= Single submitter autosomal recessive nonsyndromic hearing loss 8
  • p.Glu408fs Single submitter hearing loss disorder
  • p.Glu445Lys Single submitter TMPRSS3-related disorder ⚠
  • p.His257Gln Single submitter autosomal recessive nonsyndromic hearing loss 8 ⚠
  • p.His444= Single submitter autosomal recessive nonsyndromic hearing loss 8
  • p.Ile422= Single submitter autosomal recessive nonsyndromic hearing loss 8
  • p.Met319Ile Single submitter Inborn genetic diseases ⚠
  • p.Met383Ile Single submitter autosomal recessive nonsyndromic hearing loss 8 ⚠
  • p.Met383Lys Single submitter TMPRSS3-related disorder ⚠
  • p.Phe71= Single submitter Inborn genetic diseases
  • p.Phe71Ser Single submitter autosomal recessive nonsyndromic hearing loss 8
  • p.Pro333= Single submitter
  • p.Pro430Ser Single submitter autosomal recessive nonsyndromic hearing loss 8 ⚠
  • p.Ser160Leu Single submitter Inborn genetic diseases ⚠
  • p.Ser96Leu Single submitter Inborn genetic diseases ⚠
  • p.Ter454Arg Single submitter autosomal recessive nonsyndromic hearing loss 8
  • p.Trp343Leu Single submitter ⚠
  • p.Tyr137= Single submitter autosomal recessive nonsyndromic hearing loss 8
  • p.Tyr239His Single submitter autosomal recessive nonsyndromic hearing loss 8 ⚠
  • p.Tyr263= Single submitter autosomal recessive nonsyndromic hearing loss 8
  • p.Tyr375= Single submitter autosomal recessive nonsyndromic hearing loss 8
  • p.Val116Ala Single submitter Inborn genetic diseases ⚠
  • p.Val199Met Single submitter TMPRSS3-related disorder ⚠
  • p.Val291Leu Single submitter autosomal recessive nonsyndromic hearing loss 8 ⚠
  • p.Val436Ile Single submitter autosomal recessive nonsyndromic hearing loss 8 ⚠

Benign 43

Benign/Likely benign 11

  • c.323-8T>C Multiple submitters
  • c.447-13A>G Multiple submitters autosomal recessive nonsyndromic hearing loss 8
  • c.-34G>A Multiple submitters autosomal recessive nonsyndromic hearing loss 8
  • c.*246G>A Multiple submitters autosomal recessive nonsyndromic hearing loss 8
  • c.*2G>A Multiple submitters autosomal recessive nonsyndromic hearing loss 8
  • p.Ala90Thr Multiple submitters autosomal recessive nonsyndromic hearing loss 8
  • p.Gln144= Multiple submitters autosomal recessive nonsyndromic hearing loss 8
  • p.Gly111Ser Multiple submitters autosomal recessive nonsyndromic hearing loss 8
  • p.Tyr77= Multiple submitters autosomal recessive nonsyndromic hearing loss 8
  • p.Val151= Multiple submitters autosomal recessive nonsyndromic hearing loss 8
  • p.Val53Ile Multiple submitters autosomal recessive nonsyndromic hearing loss 8

Likely benign 259

Uncertain significance 161