HNMT — 58 ClinVar variants

All ClinVar germline HNMT variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 32 flagged for review →

1 Pathogenic · 2 Likely pathogenic · 2 Conflicting · 1 Benign · 1 Benign/Likely benign · 15 Likely benign · 36 Uncertain significance

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

⚑ Evidence disagreements 32

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 agree, ClinVar conflicts 1

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

HNMT p.Glu109Lys Conflicting Single submitter
intellectual disability, autosomal recessive 51

Predictors lean, ClinVar uncertain 27

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

Predictors split 4

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

All HNMT variants

Pathogenic 1

p.Gly60Asp No assertion criteria intellectual disability, autosomal recessive 51

Likely pathogenic 2

p.Leu208Pro Multiple submitters Paediatric disorders
p.Tyr147His Single submitter intellectual disability, autosomal recessive 51

Conflicting classifications of pathogenicity 2

p.Glu109Lys Single submitter intellectual disability, autosomal recessive 51 ⚠
p.His159fs Single submitter inherited susceptibility to asthma

Benign 1

p.Glu118= Single submitter

Benign/Likely benign 1

p.Gly60= Multiple submitters

Likely benign 15

p.Tyr186= Multiple submitters
c.137+5C>A Single submitter
c.190+11042G>A Single submitter
p.Ala292= Single submitter
p.Ala92= Single submitter
p.Arg189= Single submitter
p.Glu89= Single submitter
p.Gly48= Single submitter
p.Phe250= Single submitter
p.Pro152= Single submitter
p.Thr200= Single submitter
p.Tyr15= Single submitter
p.Val111Ile Single submitter
p.Ile288Thr No assertion criteria HNMT-related disorder
p.Tyr198= No assertion criteria HNMT-related disorder

Uncertain significance 36

p.Gly48Ala Multiple submitters pulmonary arterial hypertension ⚠
p.Met1Ile Multiple submitters
c.137+2287G>A Single submitter inherited susceptibility to asthma
p.Ala114Ser Single submitter ⚠
p.Ala114Val Single submitter ⚠
p.Asn210His Single submitter ⚠
p.Asn84Ser Single submitter ⚠
p.Asp11Asn Single submitter ⚠
p.Asp180Gly Single submitter ⚠
p.Cys248Arg Single submitter ⚠
p.Gln134Arg Single submitter ⚠
p.Gly178= Single submitter intellectual disability, autosomal recessive 51
p.Gly178Val Single submitter
p.Gly42Asp Single submitter ⚠
p.Gly61Arg Single submitter ⚠
p.Gly62Asp Single submitter ⚠
p.His116Pro Single submitter ⚠
p.His159Tyr Single submitter ⚠
p.Ile171Ser Single submitter ⚠
p.Lys104Asn Single submitter ⚠
p.Lys274Arg Single submitter ⚠
p.Met36Thr Single submitter ⚠
p.Pro152Ser Single submitter ⚠
p.Pro256Ser Single submitter ⚠
p.Pro79Ser Single submitter ⚠
p.Ser106Leu Single submitter intellectual disability, autosomal recessive 51 ⚠
p.Ser120Leu Single submitter ⚠
p.Ser227Ala Single submitter ⚠
p.Ser7Asn Single submitter ⚠
p.Thr119Arg Single submitter ⚠
p.Thr119Ile Single submitter ⚠
p.Thr284Ile Single submitter ⚠
p.Thr50Ile Single submitter ⚠
p.Tyr15His Single submitter ⚠
p.Tyr186Ter Single submitter
p.Val102Ala Single submitter ⚠