CPT1C — 421 ClinVar variants

All ClinVar germline CPT1C variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 215 flagged for review →

8 Pathogenic · 9 Likely pathogenic · 11 Conflicting · 16 Benign · 6 Benign/Likely benign · 149 Likely benign · 222 Uncertain significance

Full CPT1C gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 215

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 1

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

Predictors agree, ClinVar conflicts 4

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

Predictors lean, ClinVar uncertain 103

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

Predictors split 107

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

All CPT1C variants

Pathogenic 8

  • p.Ala412fs Single submitter hereditary spastic paraplegia 73
  • p.Arg340Ter Single submitter hereditary spastic paraplegia 73
  • p.Arg557Ter Single submitter hereditary spastic paraplegia 73
  • p.Arg579fs Single submitter hereditary spastic paraplegia 73
  • p.Gln218Ter Single submitter hereditary spastic paraplegia 73
  • p.Ile686fs Single submitter hereditary spastic paraplegia 73
  • p.Tyr186Ter Single submitter hereditary spastic paraplegia 73
  • p.Arg37Cys No assertion criteria hereditary spastic paraplegia 73 ⚠

Likely pathogenic 9

  • c.1450-2A>C Single submitter hereditary spastic paraplegia 73
  • c.2019+1G>C Single submitter hereditary spastic paraplegia 73
  • c.694-2A>G Single submitter hereditary spastic paraplegia 73
  • p.Arg245Ter Single submitter hereditary spastic paraplegia 73
  • p.Arg349Ter Single submitter hereditary spastic paraplegia 73
  • p.Gln361Ter Single submitter hereditary spastic paraplegia 73
  • p.Gly552Val Single submitter
  • p.Met1Arg Single submitter hereditary spastic paraplegia 73
  • p.Gln400Ter No assertion criteria

Conflicting classifications of pathogenicity 11

  • p.Ala431= Single submitter hereditary spastic paraplegia 73
  • p.Arg285= Single submitter hereditary spastic paraplegia 73
  • p.Arg300His Single submitter hereditary spastic paraplegia 73 ⚠
  • p.Arg579Lys Single submitter hereditary spastic paraplegia 73 ⚠
  • p.Asn698Asp Single submitter hereditary spastic paraplegia 73 ⚠
  • p.Asp200Asn Single submitter hereditary spastic paraplegia 73 ⚠
  • p.Pro687Ala Single submitter hereditary spastic paraplegia 73 ⚠
  • p.Thr508Ile Single submitter hereditary spastic paraplegia 73 ⚠
  • p.Thr799Ile Single submitter hereditary spastic paraplegia 73 ⚠
  • p.Tyr436= Single submitter hereditary spastic paraplegia 73
  • p.Val632Met Single submitter hereditary spastic paraplegia 73 ⚠

Benign 16

  • c.2133+15dup Multiple submitters hereditary spastic paraplegia 73
  • c.453+14A>G Multiple submitters hereditary spastic paraplegia 73
  • p.Ala442= Multiple submitters hereditary spastic paraplegia 73
  • p.Asp498= Multiple submitters hereditary spastic paraplegia 73
  • p.Ser215= Multiple submitters hereditary spastic paraplegia 73
  • p.Thr508= Multiple submitters hereditary spastic paraplegia 73
  • c.141+10G>A Single submitter hereditary spastic paraplegia 73
  • c.1450-8G>A Single submitter hereditary spastic paraplegia 73
  • c.2133+11_2133+12insA Single submitter hereditary spastic paraplegia 73
  • c.2133+12T>G Single submitter hereditary spastic paraplegia 73
  • p.Ala407Val Single submitter hereditary spastic paraplegia 73 ⚠
  • p.Arg514Leu Single submitter hereditary spastic paraplegia 73 ⚠
  • p.Arg631= Single submitter hereditary spastic paraplegia 73
  • p.Asn461= Single submitter hereditary spastic paraplegia 73
  • p.Gly339= Single submitter hereditary spastic paraplegia 73
  • p.His332= Single submitter hereditary spastic paraplegia 73

Benign/Likely benign 6

  • c.1731+7T>A Multiple submitters hereditary spastic paraplegia 73
  • p.Ala639Thr Multiple submitters hereditary spastic paraplegia 73
  • p.Cys583= Multiple submitters hereditary spastic paraplegia 73
  • p.Met798Val Multiple submitters hereditary spastic paraplegia 73
  • p.Ser467= Multiple submitters hereditary spastic paraplegia 73
  • p.Tyr241His Multiple submitters hereditary spastic paraplegia 73

Likely benign 149

  • c.1567-10C>T Multiple submitters hereditary spastic paraplegia 73
  • c.2134-18C>T Multiple submitters hereditary spastic paraplegia 73
  • c.454-11C>T Multiple submitters hereditary spastic paraplegia 73
  • p.Arg325= Multiple submitters hereditary spastic paraplegia 73
  • p.Gln180= Multiple submitters hereditary spastic paraplegia 73
  • p.His375= Multiple submitters hereditary spastic paraplegia 73
  • p.Leu531= Multiple submitters hereditary spastic paraplegia 73
  • p.Leu693Met Multiple submitters hereditary spastic paraplegia 73
  • p.Ser646= Multiple submitters hereditary spastic paraplegia 73
  • c.1160+13G>C Single submitter hereditary spastic paraplegia 73
  • c.1160+5GGGTCAG[2] Single submitter hereditary spastic paraplegia 73
  • c.1161-12C>T Single submitter hereditary spastic paraplegia 73
  • c.1343+15G>A Single submitter hereditary spastic paraplegia 73
  • c.1344-9C>T Single submitter hereditary spastic paraplegia 73
  • c.141+19C>T Single submitter hereditary spastic paraplegia 73
  • c.142-15C>T Single submitter hereditary spastic paraplegia 73
  • c.1449+7C>T Single submitter hereditary spastic paraplegia 73
  • c.1566+8T>G Single submitter
  • c.1567-13C>T Single submitter hereditary spastic paraplegia 73
  • c.1731+10G>T Single submitter
  • c.1731+16C>T Single submitter
  • c.1732-14_1732-12del Single submitter hereditary spastic paraplegia 73
  • c.1732-16C>T Single submitter hereditary spastic paraplegia 73
  • c.1732-7C>T Single submitter hereditary spastic paraplegia 73
  • c.1732-8del Single submitter hereditary spastic paraplegia 73
  • c.1866+13C>T Single submitter hereditary spastic paraplegia 73
  • c.1866+16G>A Single submitter hereditary spastic paraplegia 73
  • c.2019+11A>C Single submitter hereditary spastic paraplegia 73
  • c.2019+11A>G Single submitter hereditary spastic paraplegia 73
  • c.2019+17A>G Single submitter hereditary spastic paraplegia 73
  • c.2133+11C>T Single submitter hereditary spastic paraplegia 73
  • c.2133+19G>C Single submitter hereditary spastic paraplegia 73
  • c.2226+7C>T Single submitter
  • c.2227-9T>C Single submitter hereditary spastic paraplegia 73
  • c.281+8C>A Single submitter hereditary spastic paraplegia 73
  • c.281+9C>T Single submitter hereditary spastic paraplegia 73
  • c.282-12C>G Single submitter hereditary spastic paraplegia 73
  • c.282-15T>C Single submitter hereditary spastic paraplegia 73
  • c.282-5C>T Single submitter hereditary spastic paraplegia 73
  • c.453+4T>C Single submitter hereditary spastic paraplegia 73
  • c.556-14C>T Single submitter hereditary spastic paraplegia 73
  • c.556-6C>T Single submitter hereditary spastic paraplegia 73
  • c.556-9C>A Single submitter hereditary spastic paraplegia 73
  • c.693+10G>A Single submitter hereditary spastic paraplegia 73
  • c.693+11C>T Single submitter hereditary spastic paraplegia 73
  • c.693+18C>T Single submitter hereditary spastic paraplegia 73
  • c.693+7C>G Single submitter hereditary spastic paraplegia 73
  • c.694-10C>G Single submitter hereditary spastic paraplegia 73
  • c.694-14C>A Single submitter hereditary spastic paraplegia 73
  • c.694-7C>T Single submitter hereditary spastic paraplegia 73
  • c.694-8G>A Single submitter hereditary spastic paraplegia 73
  • c.694-9C>G Single submitter hereditary spastic paraplegia 73
  • c.694-9C>T Single submitter hereditary spastic paraplegia 73
  • c.771+11G>A Single submitter hereditary spastic paraplegia 73
  • c.771+20G>A Single submitter hereditary spastic paraplegia 73
  • c.879+12C>T Single submitter hereditary spastic paraplegia 73
  • c.879+13C>T Single submitter
  • c.880-13C>T Single submitter hereditary spastic paraplegia 73
  • c.965-12C>T Single submitter hereditary spastic paraplegia 73
  • p.Ala107= Single submitter hereditary spastic paraplegia 73
  • p.Ala111= Single submitter hereditary spastic paraplegia 73
  • p.Ala203= Single submitter hereditary spastic paraplegia 73
  • p.Ala407= Single submitter hereditary spastic paraplegia 73
  • p.Ala411= Single submitter
  • p.Ala656= Single submitter hereditary spastic paraplegia 73
  • p.Ala7= Single submitter hereditary spastic paraplegia 73
  • p.Ala712Gly Single submitter hereditary spastic paraplegia 73 ⚠
  • p.Ala754= Single submitter hereditary spastic paraplegia 73
  • p.Arg11= Single submitter hereditary spastic paraplegia 73
  • p.Arg222= Single submitter
  • p.Arg222Gln Single submitter
  • p.Arg271= Single submitter hereditary spastic paraplegia 73
  • p.Arg300= Single submitter hereditary spastic paraplegia 73
  • p.Arg349= Single submitter hereditary spastic paraplegia 73
  • p.Arg37= Single submitter hereditary spastic paraplegia 73
  • p.Asn312= Single submitter hereditary spastic paraplegia 73
  • p.Asp322= Single submitter hereditary spastic paraplegia 73
  • p.Asp521= Single submitter hereditary spastic paraplegia 73
  • p.Asp753= Single submitter hereditary spastic paraplegia 73
  • p.Asp802Asn Single submitter
  • p.Gln516= Single submitter hereditary spastic paraplegia 73
  • p.Gln97His Single submitter hereditary spastic paraplegia 73
  • p.Glu600= Single submitter hereditary spastic paraplegia 73
  • p.Glu608= Single submitter hereditary spastic paraplegia 73
  • p.Gly462= Single submitter hereditary spastic paraplegia 73
  • p.Gly716= Single submitter hereditary spastic paraplegia 73
  • p.Gly774= Single submitter hereditary spastic paraplegia 73
  • p.Gly96= Single submitter hereditary spastic paraplegia 73
  • p.His140= Single submitter hereditary spastic paraplegia 73
  • p.His653= Single submitter
  • p.His767= Single submitter hereditary spastic paraplegia 73
  • p.His98= Single submitter hereditary spastic paraplegia 73
  • p.His99= Single submitter hereditary spastic paraplegia 73
  • p.Ile119= Single submitter hereditary spastic paraplegia 73
  • p.Ile477= Single submitter hereditary spastic paraplegia 73
  • p.Ile569= Single submitter hereditary spastic paraplegia 73
  • p.Ile722Asn Single submitter hereditary spastic paraplegia 73 ⚠
  • p.Ile729= Single submitter hereditary spastic paraplegia 73
  • p.Leu130Val Single submitter hereditary spastic paraplegia 73 ⚠
  • p.Leu280= Single submitter hereditary spastic paraplegia 73
  • p.Leu281= Single submitter
  • p.Leu424= Single submitter hereditary spastic paraplegia 73
  • p.Leu433= Single submitter hereditary spastic paraplegia 73
  • p.Leu537= Single submitter
  • p.Leu550= Single submitter hereditary spastic paraplegia 73
  • p.Leu593= Single submitter hereditary spastic paraplegia 73
  • p.Leu60= Single submitter hereditary spastic paraplegia 73
  • p.Leu640= Single submitter hereditary spastic paraplegia 73
  • p.Leu654= Single submitter hereditary spastic paraplegia 73
  • p.Leu756= Single submitter hereditary spastic paraplegia 73
  • p.Pro139= Single submitter
  • p.Pro146= Single submitter hereditary spastic paraplegia 73
  • p.Pro175= Single submitter hereditary spastic paraplegia 73
  • p.Pro247= Single submitter hereditary spastic paraplegia 73
  • p.Pro292Leu Single submitter
  • p.Pro421= Single submitter hereditary spastic paraplegia 73
  • p.Pro505= Single submitter hereditary spastic paraplegia 73
  • p.Ser13= Single submitter hereditary spastic paraplegia 73
  • p.Ser131= Single submitter hereditary spastic paraplegia 73
  • p.Ser144= Single submitter hereditary spastic paraplegia 73
  • p.Ser158= Single submitter hereditary spastic paraplegia 73
  • p.Ser178= Single submitter
  • p.Ser189= Single submitter hereditary spastic paraplegia 73
  • p.Ser432= Single submitter hereditary spastic paraplegia 73
  • p.Ser549= Single submitter hereditary spastic paraplegia 73
  • p.Ser562= Single submitter hereditary spastic paraplegia 73
  • p.Ser588= Single submitter hereditary spastic paraplegia 73
  • p.Ser668= Single submitter hereditary spastic paraplegia 73
  • p.Ser797= Single submitter hereditary spastic paraplegia 73
  • p.Thr121= Single submitter hereditary spastic paraplegia 73
  • p.Thr265= Single submitter hereditary spastic paraplegia 73
  • p.Thr265Pro Single submitter hereditary spastic paraplegia 73
  • p.Thr314= Single submitter hereditary spastic paraplegia 73
  • p.Thr389= Single submitter hereditary spastic paraplegia 73
  • p.Thr455= Single submitter hereditary spastic paraplegia 73
  • p.Thr52= Single submitter hereditary spastic paraplegia 73
  • p.Thr601= Single submitter hereditary spastic paraplegia 73
  • p.Thr606= Single submitter hereditary spastic paraplegia 73
  • p.Thr730= Single submitter hereditary spastic paraplegia 73
  • p.Tyr323= Single submitter hereditary spastic paraplegia 73
  • p.Tyr495= Single submitter hereditary spastic paraplegia 73
  • p.Tyr586= Single submitter hereditary spastic paraplegia 73
  • p.Val104= Single submitter hereditary spastic paraplegia 73
  • p.Val124= Single submitter hereditary spastic paraplegia 73
  • p.Val262= Single submitter hereditary spastic paraplegia 73
  • p.Val276= Single submitter
  • p.Val541= Single submitter hereditary spastic paraplegia 73
  • p.Val545= Single submitter hereditary spastic paraplegia 73
  • p.Phe594= No assertion criteria CPT1C-related disorder

Uncertain significance 222