CSF1R — 990 ClinVar variants

All ClinVar germline CSF1R variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 400 flagged for review →

42 Pathogenic · 5 Pathogenic/Likely pathogenic · 35 Likely pathogenic · 62 Conflicting · 105 Benign · 19 Benign/Likely benign · 310 Likely benign · 412 Uncertain significance

Full CSF1R gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 400

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 26

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

Predicted LoF vs a conflicting call 1

ClinVar submitters conflict, and it's a predicted loss-of-function change in a gene where LoF causes disease — flagged for review, not resolved (verify NMD-escape for C-terminal truncations). Non-missense.

Predictors lean, ClinVar uncertain 183

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification. · showing the 150 best-reviewed of 183

Predictors split 189

The independent predictors disagree with each other — read with care. · showing the 150 best-reviewed of 189

All CSF1R variants

Pathogenic 42

  • p.Ala781Val Multiple submitters leukoencephalopathy, hereditary diffuse, with spheroids
  • p.Arg676Ter Multiple submitters leukoencephalopathy, diffuse hereditary, with spheroids 1
  • p.Arg777Gln Multiple submitters leukoencephalopathy, diffuse hereditary, with spheroids 1
  • p.Gln481Ter Multiple submitters leukoencephalopathy, hereditary diffuse, with spheroids
  • p.Tyr540Ter Multiple submitters brain abnormalities, neurodegeneration, and dysosteosclerosis
  • c.1969+115_1969+116del Single submitter brain abnormalities, neurodegeneration, and dysosteosclerosis
  • c.1969+1G>A Single submitter leukoencephalopathy, hereditary diffuse, with spheroids
  • p.Ala770Pro Single submitter
  • p.Arg777Trp Single submitter leukoencephalopathy, hereditary diffuse, with spheroids
  • p.Cys278Ter Single submitter
  • p.Gln426fs Single submitter
  • p.Gln642Ter Single submitter
  • p.Glu626Ter Single submitter
  • p.Glu739fs Single submitter
  • p.Glu847Lys Single submitter
  • p.Gly589Glu Single submitter
  • p.His790fs Single submitter
  • p.Lys185fs Single submitter Inborn genetic diseases
  • p.Lys350fs Single submitter
  • p.Lys706fs Single submitter
  • p.Met875Thr Single submitter leukoencephalopathy, hereditary diffuse, with spheroids
  • p.Pro824Leu Single submitter leukoencephalopathy, diffuse hereditary, with spheroids 1
  • p.Ser367fs Single submitter
  • p.Ser55fs Single submitter
  • p.Ser686fs Single submitter
  • p.Ser850Ter Single submitter brain abnormalities, neurodegeneration, and dysosteosclerosis
  • p.Thr567fs Single submitter leukoencephalopathy, hereditary diffuse, with spheroids
  • p.Thr81fs Single submitter
  • p.Thr833Lys Single submitter leukoencephalopathy, hereditary diffuse, with spheroids
  • p.Trp58Ter Single submitter
  • p.Tyr561Ter Single submitter
  • p.Val831fs Single submitter
  • c.1754-1G>C No assertion criteria brain abnormalities, neurodegeneration, and dysosteosclerosis
  • c.1754-2A>G No assertion criteria leukoencephalopathy, hereditary diffuse, with spheroids
  • c.2442+1G>T No assertion criteria leukoencephalopathy, hereditary diffuse, with spheroids
  • c.2467C>T No assertion criteria leukoencephalopathy, hereditary diffuse, with spheroids
  • c.2655-2A>G No assertion criteria leukoencephalopathy, hereditary diffuse, with spheroids
  • p.Ala781Glu No assertion criteria leukoencephalopathy, hereditary diffuse, with spheroids
  • p.Asp837Tyr No assertion criteria leukoencephalopathy, hereditary diffuse, with spheroids
  • p.Ile843_Leu844delinsGlyIle No assertion criteria leukoencephalopathy, hereditary diffuse, with spheroids
  • p.Phe828Ser No assertion criteria leukoencephalopathy, hereditary diffuse, with spheroids
  • p.Ser688fs No assertion criteria leukoencephalopathy, hereditary diffuse, with spheroids

Pathogenic/Likely pathogenic 5

  • p.Arg782Cys Multiple submitters leukoencephalopathy, diffuse hereditary, with spheroids 1
  • p.Arg782His Multiple submitters brain abnormalities, neurodegeneration, and dysosteosclerosis
  • p.Glu633Lys Multiple submitters leukoencephalopathy, diffuse hereditary, with spheroids 1
  • p.Gly589Arg Multiple submitters leukoencephalopathy, diffuse hereditary, with spheroids 1
  • p.Ile794Thr Multiple submitters leukoencephalopathy, diffuse hereditary, with spheroids 1

Likely pathogenic 35

  • p.Ala780Val Multiple submitters leukoencephalopathy, diffuse hereditary, with spheroids 1
  • p.Gln877Ter Multiple submitters leukoencephalopathy, hereditary diffuse, with spheroids
  • p.Gly591Glu Multiple submitters leukoencephalopathy, diffuse hereditary, with spheroids 1
  • c.1082+1G>A Single submitter
  • c.2132+2T>C Single submitter
  • c.2442+2T>C Single submitter
  • p.Ala681fs Single submitter leukoencephalopathy, diffuse hereditary, with spheroids 1
  • p.Ala763Thr Single submitter leukoencephalopathy, diffuse hereditary, with spheroids 1
  • p.Ala792Asp Single submitter
  • p.Ala823Thr Single submitter leukoencephalopathy, hereditary diffuse, with spheroids
  • p.Ala891Pro Single submitter Alzheimer disease
  • p.Arg782Leu Single submitter
  • p.Asp802Gly Single submitter brain abnormalities, neurodegeneration, and dysosteosclerosis
  • p.Gln311Ter Single submitter leukoencephalopathy, diffuse hereditary, with spheroids 1
  • p.Gln835Ter Single submitter leukoencephalopathy, diffuse hereditary, with spheroids 1
  • p.Glu24fs Single submitter brain abnormalities, neurodegeneration, and dysosteosclerosis
  • p.Glu403Ter Single submitter
  • p.Glu664Lys Single submitter
  • p.Glu664Val Single submitter leukoencephalopathy, diffuse hereditary, with spheroids 1
  • p.Glu847Gln Single submitter
  • p.His776Tyr Single submitter Alzheimer disease
  • p.Ile646Asn Single submitter leukoencephalopathy, diffuse hereditary, with spheroids 1
  • p.Ile794Phe Single submitter
  • p.Leu817Gln Single submitter
  • p.Lys357Ter Single submitter leukoencephalopathy, hereditary diffuse, with spheroids
  • p.Phe849Ile Single submitter brain abnormalities, neurodegeneration, and dysosteosclerosis
  • p.Pro818His Single submitter leukoencephalopathy, diffuse hereditary, with spheroids 1
  • p.Pro824Arg Single submitter
  • p.Pro855Thr Single submitter leukoencephalopathy, diffuse hereditary, with spheroids 1
  • p.Ser281fs Single submitter
  • p.Tyr276Ter Single submitter brain abnormalities, neurodegeneration, and dysosteosclerosis
  • p.Tyr923Cys Single submitter leukoencephalopathy, diffuse hereditary, with spheroids 1 ⚠
  • p.Val613Met Single submitter leukoencephalopathy, diffuse hereditary, with spheroids 1
  • p.Lys793Glu No assertion criteria leukoencephalopathy, diffuse hereditary, with spheroids 1
  • p.Phe849Ser No assertion criteria CSF1R-related leukoencephalopathy

Conflicting classifications of pathogenicity 62

Benign 105

Benign/Likely benign 19

  • c.1626+3G>A Multiple submitters Inborn genetic diseases
  • c.1753+7T>C Multiple submitters
  • c.593-9C>T Multiple submitters leukoencephalopathy, hereditary diffuse, with spheroids
  • p.Ala123Gly Multiple submitters CSF1R-related disorder ⚠
  • p.Cys954= Multiple submitters leukoencephalopathy, hereditary diffuse, with spheroids
  • p.Glu920Asp Multiple submitters leukoencephalopathy, hereditary diffuse, with spheroids
  • p.His643= Multiple submitters brain abnormalities, neurodegeneration, and dysosteosclerosis
  • p.Ile646= Multiple submitters brain abnormalities, neurodegeneration, and dysosteosclerosis
  • p.Leu536Val Multiple submitters leukoencephalopathy, hereditary diffuse, with spheroids
  • p.Leu60= Multiple submitters leukoencephalopathy, hereditary diffuse, with spheroids
  • p.Ser935= Multiple submitters leukoencephalopathy, hereditary diffuse, with spheroids
  • p.Ser94= Multiple submitters leukoencephalopathy, hereditary diffuse, with spheroids
  • p.Thr314= Multiple submitters
  • p.Thr722= Multiple submitters leukoencephalopathy, hereditary diffuse, with spheroids
  • p.Thr75Ile Multiple submitters leukoencephalopathy, hereditary diffuse, with spheroids ⚠
  • p.Val268Ile Multiple submitters leukoencephalopathy, hereditary diffuse, with spheroids ⚠
  • p.Val32Gly Multiple submitters leukoencephalopathy, hereditary diffuse, with spheroids ⚠
  • p.Val406Ile Multiple submitters Inborn genetic diseases ⚠
  • p.Val468= Multiple submitters leukoencephalopathy, hereditary diffuse, with spheroids

Likely benign 310

Showing the top 300 by review status; the full set is in the sitemap.

Uncertain significance 412

Showing the top 300 by review status; the full set is in the sitemap.