GNRHR — 217 ClinVar variants

All ClinVar germline GNRHR variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 66 flagged for review →

19 Pathogenic · 13 Pathogenic/Likely pathogenic · 15 Likely pathogenic · 7 Conflicting · 18 Benign · 5 Benign/Likely benign · 17 Likely benign · 123 Uncertain significance

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

⚑ Evidence disagreements 66

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 3

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

Predictors lean, ClinVar uncertain 42

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

Predictors split 17

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

All GNRHR variants

Pathogenic 19

  • p.Ala129Asp Multiple submitters hypogonadotropic hypogonadism 7 with or without anosmia
  • p.Ala171Thr Multiple submitters GNRHR-related disorders ⚠
  • p.Arg139His Multiple submitters GNRHR-related disorders
  • p.Arg38Ter Multiple submitters GNRHR-related disorders
  • p.Ser168Arg Multiple submitters hypogonadotropic hypogonadism 7 with or without anosmia ⚠
  • p.Thr269Met Multiple submitters hypogonadotropic hypogonadism 7 with or without anosmia ⚠
  • p.Val134Gly Multiple submitters hypogonadotropic hypogonadism 7 with or without anosmia
  • c.523-1G>A Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • p.Arg139Cys Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • p.Asn12fs Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • p.Cys200Tyr Single submitter GNRHR-related disorders ⚠
  • p.Gln174Arg Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • p.Tyr211Ter Single submitter
  • p.Val39fs Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • p.Leu314Ter No assertion criteria hypogonadotropic hypogonadism 7 with or without anosmia
  • p.Met131Thr No assertion criteria hypogonadotropic hypogonadism 7 with or without anosmia
  • p.Pro320Leu No assertion criteria hypogonadotropic hypogonadism 7 with or without anosmia
  • p.Ser217Arg No assertion criteria hypogonadotropic hypogonadism 7 with or without anosmia
  • p.Thr281Ile No assertion criteria hypogonadotropic hypogonadism 7 with or without anosmia ⚠

Pathogenic/Likely pathogenic 13

  • c.742+2T>C Multiple submitters hypogonadotropic hypogonadism
  • p.Arg262Gln Multiple submitters GNRHR-related disorders ⚠
  • p.Arg262Trp Multiple submitters hypogonadotropic hypogonadism 7 with or without anosmia
  • p.Asn10_Gln11delinsLysLys Multiple submitters GNRHR-related disorders
  • p.Asn10Lys Multiple submitters Isolated GnRH Deficiency ⚠
  • p.Cys279Tyr Multiple submitters
  • p.Gln106Arg Multiple submitters GNRHR-related disorders
  • p.Glu90Lys Multiple submitters hypogonadotropic hypogonadism 7 with or without anosmia ⚠
  • p.Leu117Arg Multiple submitters hypogonadotropic hypogonadism 7 with or without anosmia
  • p.Leu266Arg Multiple submitters GNRHR-related disorders
  • p.Phe309del Multiple submitters GNRHR-related disorders
  • p.Ser118fs Multiple submitters isolated congenital hypogonadotropic hypogonadism
  • p.Tyr283His Multiple submitters hypogonadotropic hypogonadism 7 with or without anosmia ⚠

Likely pathogenic 15

  • p.Arg38Gln Multiple submitters GNRHR-related disorders ⚠
  • p.Gln157Ter Multiple submitters hypogonadotropic hypogonadism 7 with or without anosmia
  • p.Tyr284Cys Multiple submitters hypogonadotropic hypogonadism 7 with or without anosmia
  • c.743-1G>A Single submitter
  • p.Ala163Asp Single submitter
  • p.Ala171Val Single submitter
  • p.Asp138Gly Single submitter
  • p.Gln195Ter Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • p.Ile93fs Single submitter
  • p.Leu137Pro Single submitter GNRHR-related disorders
  • p.Leu166Pro Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • p.Leu83fs Single submitter
  • p.Phe52fs Single submitter
  • p.Pro282Leu Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • p.Pro259= No assertion criteria GNRHR-related disorder

Conflicting classifications of pathogenicity 7

  • c.523-15del Single submitter
  • p.Arg240Gln Single submitter hypogonadotropic hypogonadism 7 with or without anosmia ⚠
  • p.Gln11Lys Single submitter Isolated GnRH Deficiency ⚠
  • p.Ile222= Single submitter Inborn genetic diseases
  • p.Phe216= Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • p.Pro146Ser Single submitter hypogonadotropic hypogonadism 7 with or without anosmia ⚠
  • p.Val94Ala Single submitter hypogonadotropic hypogonadism 7 with or without anosmia ⚠

Benign 18

  • c.742+35C>T Multiple submitters
  • c.-1497C>T Multiple submitters hypogonadotropic hypogonadism 7 with or without anosmia
  • c.-224A>G Multiple submitters hypogonadotropic hypogonadism 7 with or without anosmia
  • c.-904A>G Multiple submitters hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*1260G>T Multiple submitters hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*583A>G Multiple submitters hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*802G>C Multiple submitters hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*809C>T Multiple submitters hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*829T>C Multiple submitters hypogonadotropic hypogonadism 7 with or without anosmia
  • c.-1144T>C Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.-1255T>C Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.-1279G>A Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*1891T>G Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*2055G>A Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*2166G>A Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*2496G>A Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*2663G>T Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • p.Ser327= Single submitter

Benign/Likely benign 5

  • c.742+17G>A Multiple submitters
  • c.-1570C>G Multiple submitters hypogonadotropic hypogonadism 7 with or without anosmia
  • c.-62G>A Multiple submitters hypogonadotropic hypogonadism 7 with or without anosmia
  • p.Leu48= Multiple submitters hypogonadotropic hypogonadism 7 with or without anosmia
  • p.Ser151= Multiple submitters hypogonadotropic hypogonadism 7 with or without anosmia

Likely benign 17

  • c.-541G>A Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.-731C>T Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*2441T>C Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*2767T>C Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*385A>G Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*78G>A Single submitter
  • p.Ala261= Single submitter
  • p.Ala50= Single submitter
  • p.His247= Single submitter Inborn genetic diseases
  • p.Ile17= Single submitter
  • p.Leu238= Single submitter Inborn genetic diseases
  • p.Leu58= Single submitter
  • p.Thr144= Single submitter
  • p.Tyr176= Single submitter
  • p.Tyr323= Single submitter
  • p.Val160Ile Single submitter Inborn genetic diseases
  • p.Thr40= No assertion criteria GNRHR-related disorder

Uncertain significance 123

  • c.-8G>A Multiple submitters hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*495T>C Multiple submitters hypogonadotropic hypogonadism 7 with or without anosmia
  • p.Ala127Val Multiple submitters Inborn genetic diseases ⚠
  • p.Leu48Pro Multiple submitters Inborn genetic diseases ⚠
  • p.Met1Thr Multiple submitters hypogonadotropic hypogonadism 7 with or without anosmia
  • p.Thr237Asn Multiple submitters Inborn genetic diseases ⚠
  • p.Trp63Arg Multiple submitters Inborn genetic diseases ⚠
  • p.Trp63Cys Multiple submitters Inborn genetic diseases
  • c.743-9A>G Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.-1059G>C Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.-107C>T Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.-1239T>A Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.-1251T>C Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.-1319C>T Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.-1434A>T Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.-1464G>A Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.-1563T>C Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.-1636T>C Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.-1701A>C Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.-1702A>G Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.-1741G>T Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.-576G>T Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.-699T>C Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.-721A>G Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.-877C>A Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.-922A>G Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.-927C>T Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.-962G>A Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.-980G>A Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*1144A>G Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*1193C>T Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*1248A>C Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*1275G>A Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*1301A>G Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*1302G>C Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*1347A>G Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*1532C>A Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*1654C>T Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*1797A>G Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*1892C>A Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*193A>G Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*1948C>T Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*1984T>C Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*2165A>G Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*2196G>A Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*2244T>C Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*2248T>C Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*2328A>T Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*2588C>T Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*2748C>T Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*2772A>G Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*2802T>C Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*2919A>G Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*3011T>C Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*3076T>C Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*349A>C Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*466T>G Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*474T>C Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*622T>C Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*662T>C Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*668G>A Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*696A>T Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*730T>C Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*806G>C Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*819A>T Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*832T>C Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*912C>T Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • c.*928C>A Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • p.Ala129Val Single submitter
  • p.Arg139Leu Single submitter ⚠
  • p.Arg240Trp Single submitter ⚠
  • p.Arg75Ser Single submitter Inborn genetic diseases ⚠
  • p.Asn10Ser Single submitter ⚠
  • p.Asn3Lys Single submitter Inborn genetic diseases ⚠
  • p.Cys218Arg Single submitter Inborn genetic diseases ⚠
  • p.Gln25Lys Single submitter ⚠
  • p.Glu68Lys Single submitter Inborn genetic diseases ⚠
  • p.His182Leu Single submitter Inborn genetic diseases ⚠
  • p.His199Arg Single submitter Inborn genetic diseases ⚠
  • p.His243Pro Single submitter ⚠
  • p.Ile226Thr Single submitter ⚠
  • p.Ile258Thr Single submitter hypogonadotropic hypogonadism 7 with or without anosmia ⚠
  • p.Ile288Asn Single submitter Inborn genetic diseases ⚠
  • p.Leu228Pro Single submitter Inborn genetic diseases ⚠
  • p.Leu249Pro Single submitter Inborn genetic diseases ⚠
  • p.Leu251Gln Single submitter Inborn genetic diseases ⚠
  • p.Leu83Val Single submitter ⚠
  • p.Lys154Glu Single submitter Inborn genetic diseases ⚠
  • p.Lys72Arg Single submitter hypogonadotropic hypogonadism 7 with or without anosmia ⚠
  • p.Met100Arg Single submitter ⚠
  • p.Met125Val Single submitter Inborn genetic diseases ⚠
  • p.Met159Ile Single submitter Inborn genetic diseases ⚠
  • p.Met180Ile Single submitter Inborn genetic diseases ⚠
  • p.Met268Thr Single submitter Inborn genetic diseases ⚠
  • p.Met296Ile Single submitter Inborn genetic diseases
  • p.Met296Lys Single submitter ⚠
  • p.Met95Ile Single submitter ⚠
  • p.Met95Val Single submitter ⚠
  • p.Phe178Cys Single submitter ⚠
  • p.Phe213Tyr Single submitter Inborn genetic diseases ⚠
  • p.Ser124Tyr Single submitter Inborn genetic diseases ⚠
  • p.Ser327Cys Single submitter Inborn genetic diseases ⚠
  • p.Ser4Arg Single submitter hypogonadotropic hypogonadism 7 with or without anosmia ⚠
  • p.Ser4Thr Single submitter Inborn genetic diseases ⚠
  • p.Thr144Pro Single submitter
  • p.Thr237Ile Single submitter ⚠
  • p.Thr274= Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • p.Thr274Ala Single submitter ⚠
  • p.Thr30Ile Single submitter Inborn genetic diseases ⚠
  • p.Thr30Ser Single submitter Inborn genetic diseases ⚠
  • p.Thr32Ala Single submitter hypogonadotropic hypogonadism 7 with or without anosmia ⚠
  • p.Trp107Arg Single submitter ⚠
  • p.Trp205Arg Single submitter Inborn genetic diseases ⚠
  • p.Trp205Cys Single submitter Inborn genetic diseases ⚠
  • p.Trp280Cys Single submitter ⚠
  • p.Tyr283Ser Single submitter ⚠
  • p.Tyr290His Single submitter ⚠
  • p.Val133= Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • p.Val134Ala Single submitter ⚠
  • p.Val155= Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • p.Val192= Single submitter hypogonadotropic hypogonadism 7 with or without anosmia
  • p.Val270Ile Single submitter Inborn genetic diseases ⚠
  • p.Val304Leu Single submitter Inborn genetic diseases ⚠