NPC2 — 278 ClinVar variants

All ClinVar germline NPC2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 48 flagged for review →

22 Pathogenic · 6 Pathogenic/Likely pathogenic · 28 Likely pathogenic · 13 Conflicting · 5 Benign · 5 Benign/Likely benign · 133 Likely benign · 66 Uncertain significance

Full NPC2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 48

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 2

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

Predictors lean, ClinVar uncertain 36

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

All NPC2 variants

Pathogenic 22

  • p.Cys47Ter Multiple submitters Inborn genetic diseases
  • p.Cys99Arg Multiple submitters Niemann-Pick disease, type C2
  • p.Glu118Ter Multiple submitters Niemann-Pick disease type C
  • p.Glu20Ter Multiple submitters Inborn genetic diseases
  • p.Tyr55Ter Multiple submitters Niemann-Pick disease, type C2
  • p.Ala5fs Single submitter Niemann-Pick disease, type C2
  • p.Asn111fs Single submitter Niemann-Pick disease, type C2
  • p.Cys27fs Single submitter Niemann-Pick disease, type C2
  • p.Gln136Ter Single submitter Niemann-Pick disease, type C2
  • p.Gln146Ter Single submitter Niemann-Pick disease type C
  • p.Gln53Ter Single submitter Niemann-Pick disease, type C2
  • p.Glu36Ter Single submitter Niemann-Pick disease, type C2
  • p.Ile97fs Single submitter Niemann-Pick disease
  • p.Met1Arg Single submitter Niemann-Pick disease, type C2
  • p.Met1Lys Single submitter Niemann-Pick disease, type C2
  • p.Ser95fs Single submitter Niemann-Pick disease, type C2
  • p.Thr44fs Single submitter Niemann-Pick disease, type C2
  • p.Trp141Ter Single submitter Niemann-Pick disease, type C2
  • c.82+2T>C No assertion criteria Niemann-Pick disease, type C2
  • p.Leu10fs No assertion criteria Niemann-Pick disease, type C2
  • p.Ser67Pro No assertion criteria Niemann-Pick disease, type C2
  • p.Thr7fs No assertion criteria Niemann-Pick disease, type C2

Pathogenic/Likely pathogenic 6

  • c.190+5G>A Multiple submitters Niemann-Pick disease, type C2
  • p.Ala72fs Multiple submitters Niemann-Pick disease, type C2
  • p.Gln45Ter Multiple submitters Niemann-Pick disease type C
  • p.Lys94Ter Multiple submitters Niemann-Pick disease type C
  • p.Met1Ile Multiple submitters Niemann-Pick disease type C
  • p.Pro120Ser Multiple submitters Niemann-Pick disease type C

Likely pathogenic 28

  • c.190+1G>C Single submitter Niemann-Pick disease, type C2
  • c.191-1_193del Single submitter Niemann-Pick disease, type C2
  • c.191-1G>A Single submitter Niemann-Pick disease, type C2
  • c.363+1G>A Single submitter Niemann-Pick disease, type C2
  • c.364-2A>G Single submitter Niemann-Pick disease, type C2
  • c.83-2A>T Single submitter Niemann-Pick disease, type C2
  • p.Asp31fs Single submitter Niemann-Pick disease, type C2
  • p.Cys99Ter Single submitter Niemann-Pick disease, type C2
  • p.Cys99Trp Single submitter Niemann-Pick disease, type C2
  • p.Gln102Ter Single submitter Niemann-Pick disease, type C2
  • p.Gln23Ter Single submitter Niemann-Pick disease, type C2
  • p.Gln48Ter Single submitter Niemann-Pick disease, type C2
  • p.Gly52Ter Single submitter Niemann-Pick disease, type C2
  • p.Lys112fs Single submitter Niemann-Pick disease, type C2
  • p.Lys112Ter Single submitter Niemann-Pick disease, type C2
  • p.Lys68Ter Single submitter Niemann-Pick disease, type C2
  • p.Pro84fs Single submitter Niemann-Pick disease, type C2
  • p.Ser40Ter Single submitter Niemann-Pick disease, type C2
  • p.Ser50fs Single submitter Niemann-Pick disease, type C2
  • p.Ter152LeuextTer? Single submitter Niemann-Pick disease, type C2
  • p.Thr62fs Single submitter Niemann-Pick disease, type C2
  • p.Tyr109fs Single submitter Niemann-Pick disease, type C2
  • p.Tyr119Ter Single submitter Niemann-Pick disease, type C2
  • p.Val22fs Single submitter Niemann-Pick disease, type C2
  • p.Val30fs Single submitter Niemann-Pick disease, type C2
  • p.Val73fs Single submitter Niemann-Pick disease, type C2
  • p.Met1Thr No assertion criteria Niemann-Pick disease, type C2
  • p.Met1Val No assertion criteria Niemann-Pick disease, type C2

Conflicting classifications of pathogenicity 13

  • c.191-8T>C Single submitter Niemann-Pick disease, type C2
  • c.363+7G>A Single submitter Niemann-Pick disease, type C2
  • c.441+1G>A Single submitter Niemann-Pick disease, type C2
  • c.*295C>G Single submitter Niemann-Pick disease, type C1
  • p.Asp91= Single submitter Inborn genetic diseases
  • p.Cys140del Single submitter Niemann-Pick disease, type C2
  • p.Cys93Phe Single submitter Niemann-Pick disease, type C2 ⚠
  • p.Gly80= Single submitter Niemann-Pick disease, type C2
  • p.His150= Single submitter Inborn genetic diseases
  • p.Pro120Thr Single submitter Niemann-Pick disease, type C2 ⚠
  • p.Pro88= Single submitter Inborn genetic diseases
  • p.Pro90= Single submitter Inborn genetic diseases
  • p.Ser56= Single submitter Inborn genetic diseases

Benign 5

Benign/Likely benign 5

  • c.190+14G>A Multiple submitters Niemann-Pick disease, type C2
  • c.442-4A>C Multiple submitters Niemann-Pick disease, type C2
  • c.*271C>T Multiple submitters Niemann-Pick disease, type C1
  • c.*9T>C Multiple submitters Niemann-Pick disease, type C1
  • p.Val30Met Multiple submitters Niemann-Pick disease, type C2

Likely benign 133

  • c.441+68C>T Multiple submitters
  • p.Ala72= Multiple submitters Inborn genetic diseases
  • p.Leu10= Multiple submitters Inborn genetic diseases
  • p.Leu110= Multiple submitters Inborn genetic diseases
  • p.Pro41= Multiple submitters Niemann-Pick disease, type C2
  • p.Pro43= Multiple submitters Niemann-Pick disease, type C2
  • c.190+14G>T Single submitter Niemann-Pick disease, type C2
  • c.190+16T>C Single submitter Niemann-Pick disease, type C2
  • c.190+17C>G Single submitter Niemann-Pick disease, type C2
  • c.190+17C>T Single submitter Niemann-Pick disease, type C2
  • c.190+6dup Single submitter Niemann-Pick disease, type C2
  • c.191-10T>C Single submitter Niemann-Pick disease, type C2
  • c.191-14T>C Single submitter Niemann-Pick disease, type C2
  • c.191-187_191-186insTTG Single submitter
  • c.191-18del Single submitter Niemann-Pick disease, type C2
  • c.191-18T>C Single submitter Niemann-Pick disease, type C2
  • c.191-260G>A Single submitter
  • c.191-4T>A Single submitter Niemann-Pick disease, type C2
  • c.191-7C>G Single submitter Niemann-Pick disease, type C2
  • c.363+10A>G Single submitter Niemann-Pick disease, type C2
  • c.363+13A>G Single submitter Niemann-Pick disease, type C2
  • c.363+16_363+18del Single submitter Niemann-Pick disease, type C2
  • c.363+17T>C Single submitter Niemann-Pick disease, type C2
  • c.363+18T>A Single submitter Niemann-Pick disease, type C2
  • c.363+20A>G Single submitter Niemann-Pick disease, type C2
  • c.363+3A>G Single submitter
  • c.363+9T>C Single submitter Niemann-Pick disease, type C2
  • c.364-10C>T Single submitter Niemann-Pick disease, type C2
  • c.364-11T>C Single submitter Niemann-Pick disease, type C2
  • c.364-13T>C Single submitter Niemann-Pick disease, type C2
  • c.364-20T>C Single submitter Niemann-Pick disease, type C2
  • c.364-20T>G Single submitter Niemann-Pick disease, type C2
  • c.364-8T>G Single submitter Niemann-Pick disease, type C2
  • c.441+10T>C Single submitter Niemann-Pick disease, type C2
  • c.441+11C>G Single submitter Niemann-Pick disease, type C2
  • c.441+12T>C Single submitter Niemann-Pick disease, type C2
  • c.441+13G>A Single submitter Niemann-Pick disease, type C2
  • c.441+13G>T Single submitter Niemann-Pick disease, type C2
  • c.441+14G>C Single submitter Niemann-Pick disease, type C2
  • c.441+16G>T Single submitter Niemann-Pick disease, type C2
  • c.441+17G>C Single submitter Niemann-Pick disease, type C2
  • c.441+193dup Single submitter
  • c.441+8T>C Single submitter Niemann-Pick disease, type C2
  • c.441+9A>G Single submitter Niemann-Pick disease, type C2
  • c.441+9A>T Single submitter Niemann-Pick disease, type C2
  • c.442-101G>T Single submitter
  • c.442-10A>G Single submitter Niemann-Pick disease, type C2
  • c.442-13A>G Single submitter Niemann-Pick disease, type C2
  • c.442-17G>A Single submitter Niemann-Pick disease, type C2
  • c.442-17G>C Single submitter Niemann-Pick disease, type C2
  • c.442-4A>G Single submitter Niemann-Pick disease, type C2
  • c.442-8A>C Single submitter Niemann-Pick disease, type C2
  • c.442-8A>G Single submitter Niemann-Pick disease, type C2
  • c.442-9C>T Single submitter Niemann-Pick disease, type C2
  • c.82+10A>C Single submitter Niemann-Pick disease, type C2
  • c.82+12G>A Single submitter Niemann-Pick disease, type C2
  • c.82+13C>A Single submitter Niemann-Pick disease, type C2
  • c.82+15C>A Single submitter Niemann-Pick disease, type C2
  • c.82+15C>G Single submitter Niemann-Pick disease, type C2
  • c.82+15C>T Single submitter Niemann-Pick disease, type C2
  • c.82+16G>A Single submitter Niemann-Pick disease, type C2
  • c.82+17C>T Single submitter Niemann-Pick disease, type C2
  • c.82+295G>A Single submitter
  • c.82+6dup Single submitter Niemann-Pick disease, type C2
  • c.82+7C>T Single submitter Niemann-Pick disease, type C2
  • c.82+8C>G Single submitter Niemann-Pick disease, type C2
  • c.82+9C>T Single submitter Niemann-Pick disease, type C2
  • c.83-11T>C Single submitter Niemann-Pick disease, type C2
  • c.83-15A>G Single submitter Niemann-Pick disease, type C2
  • c.83-19A>G Single submitter Niemann-Pick disease, type C2
  • c.83-20A>G Single submitter Niemann-Pick disease, type C2
  • c.83-4G>A Single submitter Niemann-Pick disease, type C2
  • c.83-4G>T Single submitter Niemann-Pick disease, type C2
  • c.83-5T>C Single submitter Niemann-Pick disease, type C2
  • c.83-8T>G Single submitter Niemann-Pick disease, type C2
  • c.*154G>A Single submitter
  • c.*252del Single submitter
  • p.Ala12= Single submitter Niemann-Pick disease, type C2
  • p.Ala17= Single submitter Niemann-Pick disease, type C2
  • p.Ala19= Single submitter Niemann-Pick disease, type C2
  • p.Ala5= Single submitter Niemann-Pick disease, type C2
  • p.Ala6= Single submitter
  • p.Asn98= Single submitter Niemann-Pick disease, type C2
  • p.Asp104= Single submitter Niemann-Pick disease, type C2
  • p.Cys93= Single submitter Niemann-Pick disease, type C2
  • p.Gln131= Single submitter Niemann-Pick disease, type C2
  • p.Gln18= Single submitter Niemann-Pick disease, type C2
  • p.Gln23= Single submitter Niemann-Pick disease, type C2
  • p.Glu36= Single submitter Niemann-Pick disease, type C2
  • p.Glu89= Single submitter Niemann-Pick disease, type C2
  • p.Gly92= Single submitter Niemann-Pick disease, type C2
  • p.Ile143= Single submitter Niemann-Pick disease, type C2
  • p.Leu124= Single submitter Niemann-Pick disease, type C2
  • p.Leu13= Single submitter Niemann-Pick disease, type C2
  • p.Leu138= Single submitter Niemann-Pick disease, type C2
  • p.Leu151= Single submitter Niemann-Pick disease, type C2
  • p.Leu4= Single submitter Niemann-Pick disease, type C2
  • p.Leu49= Single submitter Niemann-Pick disease, type C2
  • p.Leu78= Single submitter Niemann-Pick disease, type C2
  • p.Leu9= Single submitter Niemann-Pick disease, type C2
  • p.Lys105= Single submitter Niemann-Pick disease, type C2
  • p.Lys94= Single submitter Inborn genetic diseases
  • p.Phe24= Single submitter Niemann-Pick disease, type C2
  • p.Phe3= Single submitter Niemann-Pick disease, type C2
  • p.Phe61= Single submitter Niemann-Pick disease, type C2
  • p.Pro100= Single submitter Niemann-Pick disease, type C2
  • p.Pro114= Single submitter Niemann-Pick disease, type C2
  • p.Pro120= Single submitter Niemann-Pick disease, type C2
  • p.Pro144= Single submitter Niemann-Pick disease, type C2
  • p.Pro21= Single submitter Niemann-Pick disease, type C2
  • p.Pro82= Single submitter Niemann-Pick disease, type C2
  • p.Pro84= Single submitter Niemann-Pick disease, type C2
  • p.Pro86= Single submitter Niemann-Pick disease, type C2
  • p.Ser117= Single submitter Niemann-Pick disease, type C2
  • p.Ser40= Single submitter Niemann-Pick disease, type C2
  • p.Ser50= Single submitter Niemann-Pick disease, type C2
  • p.Ser69= Single submitter Niemann-Pick disease, type C2
  • p.Ter152= Single submitter Niemann-Pick disease, type C2
  • p.Thr106= Single submitter Niemann-Pick disease, type C2
  • p.Thr15= Single submitter Niemann-Pick disease, type C2
  • p.Thr44= Single submitter Niemann-Pick disease, type C2
  • p.Thr62= Single submitter Niemann-Pick disease, type C2
  • p.Thr7= Single submitter Niemann-Pick disease, type C2
  • p.Tyr107= Single submitter Niemann-Pick disease, type C2
  • p.Tyr109= Single submitter Niemann-Pick disease, type C2
  • p.Tyr55= Single submitter Niemann-Pick disease, type C2
  • p.Val125= Single submitter Niemann-Pick disease, type C2
  • p.Val126= Single submitter Niemann-Pick disease, type C2
  • p.Val39= Single submitter Niemann-Pick disease, type C2
  • p.Val74= Single submitter Niemann-Pick disease, type C2
  • c.441+24G>A No assertion criteria NPC2-related disorder
  • c.-10_-9insGCG No assertion criteria NPC2-related disorder
  • p.Lys134= No assertion criteria NPC2-related disorder

Uncertain significance 66