CTSF — 301 ClinVar variants

All ClinVar germline CTSF variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 128 flagged for review →

17 Pathogenic · 1 Pathogenic/Likely pathogenic · 18 Likely pathogenic · 15 Conflicting · 19 Benign · 9 Benign/Likely benign · 92 Likely benign · 130 Uncertain significance

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

⚑ Evidence disagreements 128

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 7

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

Predictors lean, ClinVar uncertain 63

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

Predictors split 58

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

All CTSF variants

Pathogenic 17

  • p.Arg217Ter Multiple submitters Inborn genetic diseases
  • p.Ala282fs Single submitter neuronal ceroid lipofuscinosis 13
  • p.Gln222Ter Single submitter neuronal ceroid lipofuscinosis 13
  • p.Gln321Arg Single submitter neuronal ceroid lipofuscinosis 13
  • p.Gln74fs Single submitter
  • p.Gly73_Gln74insPro Single submitter
  • p.Ile416Thr Single submitter neuronal ceroid lipofuscinosis 13
  • p.Lys374fs Single submitter neuronal ceroid lipofuscinosis
  • p.Met291fs Single submitter neuronal ceroid lipofuscinosis 13
  • p.Pro126fs Single submitter neuronal ceroid lipofuscinosis 13
  • p.Ser139Ter Single submitter neuronal ceroid lipofuscinosis 13
  • p.Thr197_Tyr198insTer Single submitter neuronal ceroid lipofuscinosis
  • p.Tyr198Ter Single submitter neuronal ceroid lipofuscinosis 13
  • p.Val110fs Single submitter neuronal ceroid lipofuscinosis 13
  • c.213+1G>C No assertion criteria neuronal ceroid lipofuscinosis 13
  • p.Gly458Ala No assertion criteria neuronal ceroid lipofuscinosis 13
  • p.Ser319fs No assertion criteria neuronal ceroid lipofuscinosis 13

Pathogenic/Likely pathogenic 1

  • p.Lys331fs Multiple submitters neuronal ceroid lipofuscinosis

Likely pathogenic 18

  • c.1045+1G>T Multiple submitters Inborn genetic diseases
  • c.1165+2T>G Single submitter neuronal ceroid lipofuscinosis 13
  • c.1381-2A>G Single submitter
  • c.213+2T>A Single submitter neuronal ceroid lipofuscinosis 13
  • c.530_531+11del Single submitter neuronal ceroid lipofuscinosis 13
  • c.965-1G>A Single submitter neuronal ceroid lipofuscinosis 13
  • p.Ala56fs Single submitter neuronal ceroid lipofuscinosis
  • p.Arg44fs Single submitter neuronal ceroid lipofuscinosis
  • p.Cys424Ter Single submitter
  • p.Cys89fs Single submitter neuronal ceroid lipofuscinosis
  • p.Gln312Ter Single submitter neuronal ceroid lipofuscinosis 13
  • p.Glu202fs Single submitter neurodevelopmental disorder
  • p.Gly439fs Single submitter neuronal ceroid lipofuscinosis 13
  • p.Leu324Ser Single submitter neuronal ceroid lipofuscinosis 13
  • p.Ser36fs Single submitter neuronal ceroid lipofuscinosis
  • p.Trp296Ter Single submitter
  • p.Trp427fs Single submitter neuronal ceroid lipofuscinosis 13
  • p.Tyr231Ter Single submitter CTSF-related disorder

Conflicting classifications of pathogenicity 15

Benign 19

Benign/Likely benign 9

  • c.1231-13T>C Multiple submitters neuronal ceroid lipofuscinosis 13
  • c.1322-19G>A Multiple submitters neuronal ceroid lipofuscinosis 13
  • p.Arg421Trp Multiple submitters Inborn genetic diseases
  • p.Asn386= Multiple submitters Inborn genetic diseases
  • p.Asp456= Multiple submitters Inborn genetic diseases
  • p.Gln153Arg Multiple submitters Inborn genetic diseases
  • p.Glu199= Multiple submitters Inborn genetic diseases
  • p.Gly313= Multiple submitters Inborn genetic diseases
  • p.Ser469= Multiple submitters Inborn genetic diseases

Likely benign 92

  • c.1046-10C>T Multiple submitters neuronal ceroid lipofuscinosis 13
  • c.1166-10C>T Multiple submitters neuronal ceroid lipofuscinosis 13
  • c.1322-105T>G Multiple submitters
  • c.214-6C>T Multiple submitters neuronal ceroid lipofuscinosis 13
  • c.722-4G>A Multiple submitters neuronal ceroid lipofuscinosis 13
  • c.868-17C>G Multiple submitters neuronal ceroid lipofuscinosis 13
  • c.868-4G>A Multiple submitters neuronal ceroid lipofuscinosis 13
  • p.Ala82= Multiple submitters Inborn genetic diseases
  • p.Arg59= Multiple submitters Inborn genetic diseases
  • p.Asp443= Multiple submitters neuronal ceroid lipofuscinosis 13
  • p.Cys106= Multiple submitters Inborn genetic diseases
  • p.Gly57= Multiple submitters Inborn genetic diseases
  • p.Leu270= Multiple submitters neuronal ceroid lipofuscinosis 13
  • p.Leu324= Multiple submitters Inborn genetic diseases
  • p.Lys260= Multiple submitters Inborn genetic diseases
  • p.Ser209= Multiple submitters
  • p.Ser380= Multiple submitters neuronal ceroid lipofuscinosis 13
  • p.Ser401= Multiple submitters neuronal ceroid lipofuscinosis 13
  • p.Tyr342= Multiple submitters Inborn genetic diseases
  • c.1045+286A>G Single submitter
  • c.1165+8_1165+9del Single submitter neuronal ceroid lipofuscinosis 13
  • c.1166-7A>G Single submitter neuronal ceroid lipofuscinosis 13
  • c.1230+14C>T Single submitter neuronal ceroid lipofuscinosis 13
  • c.1231-13_1231-11del Single submitter neuronal ceroid lipofuscinosis 13
  • c.1231-15C>T Single submitter neuronal ceroid lipofuscinosis 13
  • c.1231-16C>T Single submitter neuronal ceroid lipofuscinosis 13
  • c.1231-27G>A Single submitter
  • c.1321+9C>T Single submitter neuronal ceroid lipofuscinosis 13
  • c.1322-14G>A Single submitter neuronal ceroid lipofuscinosis 13
  • c.1322-19G>C Single submitter neuronal ceroid lipofuscinosis 13
  • c.1322-20C>G Single submitter neuronal ceroid lipofuscinosis 13
  • c.1322-49G>T Single submitter
  • c.1322-95T>C Single submitter
  • c.1380+13G>A Single submitter neuronal ceroid lipofuscinosis 13
  • c.1380+14G>T Single submitter neuronal ceroid lipofuscinosis 13
  • c.1380+19del Single submitter neuronal ceroid lipofuscinosis 13
  • c.213+10C>T Single submitter neuronal ceroid lipofuscinosis 13
  • c.213+20G>A Single submitter neuronal ceroid lipofuscinosis 13
  • c.213+7A>T Single submitter neuronal ceroid lipofuscinosis 13
  • c.213+9G>A Single submitter neuronal ceroid lipofuscinosis 13
  • c.213+9G>T Single submitter neuronal ceroid lipofuscinosis 13
  • c.312+148G>C Single submitter
  • c.312+28C>T Single submitter
  • c.313-13C>T Single submitter
  • c.531+10C>T Single submitter
  • c.531+15G>C Single submitter neuronal ceroid lipofuscinosis 13
  • c.608-11T>G Single submitter neuronal ceroid lipofuscinosis 13
  • c.608-324del Single submitter
  • c.608-61A>G Single submitter
  • c.721+12G>A Single submitter neuronal ceroid lipofuscinosis 13
  • c.722-38_722-37del Single submitter
  • c.722-44T>C Single submitter
  • c.867+16dup Single submitter neuronal ceroid lipofuscinosis 13
  • c.867+7C>A Single submitter neuronal ceroid lipofuscinosis 13
  • c.867+8C>T Single submitter neuronal ceroid lipofuscinosis 13
  • c.868-7C>T Single submitter neuronal ceroid lipofuscinosis 13
  • c.964+11C>G Single submitter neuronal ceroid lipofuscinosis 13
  • c.964+9C>T Single submitter neuronal ceroid lipofuscinosis 13
  • c.*216_*218del Single submitter
  • p.Ala140= Single submitter
  • p.Ala19= Single submitter neuronal ceroid lipofuscinosis 13
  • p.Ala27= Single submitter
  • p.Ala344= Single submitter Inborn genetic diseases
  • p.Ala406= Single submitter neuronal ceroid lipofuscinosis 13
  • p.Ala41Gly Single submitter Inborn genetic diseases
  • p.Ala432= Single submitter neuronal ceroid lipofuscinosis 13
  • p.Arg421= Single submitter Inborn genetic diseases
  • p.Asn311= Single submitter neuronal ceroid lipofuscinosis 13
  • p.Glu86= Single submitter neuronal ceroid lipofuscinosis 13
  • p.His117= Single submitter neuronal ceroid lipofuscinosis 13
  • p.His414= Single submitter
  • p.Leu114= Single submitter neuronal ceroid lipofuscinosis 13
  • p.Leu14= Single submitter neuronal ceroid lipofuscinosis 13
  • p.Leu175= Single submitter neuronal ceroid lipofuscinosis 13
  • p.Leu351= Single submitter neuronal ceroid lipofuscinosis 13
  • p.Leu394= Single submitter
  • p.Leu5= Single submitter neuronal ceroid lipofuscinosis 13
  • p.Leu62= Single submitter neuronal ceroid lipofuscinosis 13
  • p.Lys130= Single submitter neuronal ceroid lipofuscinosis 13
  • p.Lys255= Single submitter neuronal ceroid lipofuscinosis 13
  • p.Lys396= Single submitter neuronal ceroid lipofuscinosis 13
  • p.Pro87= Single submitter neuronal ceroid lipofuscinosis 13
  • p.Ser150= Single submitter neuronal ceroid lipofuscinosis 13
  • p.Ser28Arg Single submitter Inborn genetic diseases
  • p.Thr162= Single submitter neuronal ceroid lipofuscinosis 13
  • p.Thr353= Single submitter
  • p.Tyr438= Single submitter neuronal ceroid lipofuscinosis 13
  • p.Val127= Single submitter neuronal ceroid lipofuscinosis 13
  • p.Val166= Single submitter
  • p.Val18Ala Single submitter Inborn genetic diseases
  • p.Val381= Single submitter neuronal ceroid lipofuscinosis 13
  • p.Val444Ile Single submitter Inborn genetic diseases

Uncertain significance 130