Sugi Variant

Sugi Variant/LHCGR

LHCGR — 255 ClinVar variants

All ClinVar germline LHCGR variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 129 flagged for review →

23 Pathogenic · 3 Pathogenic/Likely pathogenic · 9 Likely pathogenic · 17 Conflicting · 37 Benign · 7 Benign/Likely benign · 34 Likely benign · 125 Uncertain significance

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

⚑ Evidence disagreements 129

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 5

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 67

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

Predictors split 54

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

All LHCGR variants

Pathogenic 23

Pathogenic/Likely pathogenic 3

  • p.Arg124Ter Multiple submitters Leydig cell hypoplasia, type 1
  • p.Arg554Ter Multiple submitters disorder of sexual differentiation
  • p.Thr577Ile Multiple submitters familial male-limited precocious puberty ⚠

Likely pathogenic 9

Conflicting classifications of pathogenicity 17

  • c.161+9A>G Single submitter Leydig cell hypoplasia, type 1
  • c.458+3A>G Single submitter familial male-limited precocious puberty
  • c.605+52del Single submitter familial male-limited precocious puberty
  • c.681-6G>A Single submitter Leydig cell hypoplasia, type 1
  • c.*512C>T Single submitter Leydig cell hypoplasia, type 1
  • p.Ala236Val Single submitter Leydig cell hypoplasia, type 1 ⚠
  • p.Cys44= Single submitter familial male-limited precocious puberty
  • p.Cys699Ser Single submitter Leydig cell hypoplasia, type 1 ⚠
  • p.Gln190Lys Single submitter ⚠
  • p.Glu27= Single submitter familial male-limited precocious puberty
  • p.Ile599= Single submitter
  • p.Lys390Arg Single submitter ⚠
  • p.Pro224= Single submitter familial male-limited precocious puberty
  • p.Ser639Asn Single submitter Inborn genetic diseases ⚠
  • p.Tyr113Asn Single submitter familial male-limited precocious puberty ⚠
  • p.Tyr651= Single submitter familial male-limited precocious puberty
  • p.Val454Ile Single submitter Leydig cell hypoplasia, type 1 ⚠

Benign 37

Benign/Likely benign 7

  • c.*131C>T Multiple submitters Leydig cell hypoplasia, type 1
  • p.Glu557Lys Multiple submitters familial male-limited precocious puberty ⚠
  • p.Leu204= Multiple submitters familial male-limited precocious puberty
  • p.Leu337Ser Multiple submitters familial male-limited precocious puberty
  • p.Val208Ile Multiple submitters familial male-limited precocious puberty
  • c.*22T>G Single submitter Leydig cell hypoplasia, type 1
  • c.*535G>A Single submitter familial male-limited precocious puberty

Likely benign 34

Uncertain significance 125