COLQ — 632 ClinVar variants

All ClinVar germline COLQ variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 201 flagged for review →

55 Pathogenic · 16 Pathogenic/Likely pathogenic · 46 Likely pathogenic · 17 Conflicting · 66 Benign · 6 Benign/Likely benign · 187 Likely benign · 239 Uncertain significance

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

⚑ Evidence disagreements 201

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 6

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 109

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

Predictors split 82

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

All COLQ variants

Pathogenic 55

  • c.1195+1G>A Multiple submitters congenital myasthenic syndrome 5
  • c.1298+3A>G Multiple submitters congenital myasthenic syndrome
  • c.219+1G>C Multiple submitters congenital myasthenic syndrome 5
  • c.393+1G>A Multiple submitters congenital myasthenic syndrome
  • p.Arg227Ter Multiple submitters Synaptic congenital myasthenic syndromes
  • p.Arg282Ter Multiple submitters congenital myasthenic syndrome 5
  • p.Arg315Ter Multiple submitters Synaptic congenital myasthenic syndromes
  • p.Arg410Gln Multiple submitters congenital myasthenic syndrome 5 ⚠
  • p.Asn298fs Multiple submitters congenital myasthenic syndrome 5
  • p.Asn81fs Multiple submitters congenital myasthenic syndrome 5
  • p.Gln211Ter Multiple submitters congenital myasthenic syndrome 5
  • p.Glu214Ter Multiple submitters congenital myasthenic syndrome 5
  • p.Gly126fs Multiple submitters congenital myasthenic syndrome 5
  • p.Gly198fs Multiple submitters congenital myasthenic syndrome 5
  • p.Gly234Ter Multiple submitters congenital myasthenic syndrome 5
  • p.Leu53fs Multiple submitters congenital myasthenic syndrome 5
  • p.Pro265fs Multiple submitters congenital myasthenic syndrome 5
  • p.Pro361fs Multiple submitters congenital myasthenic syndrome
  • p.Ser169Ter Multiple submitters congenital myasthenic syndrome 5
  • p.Tyr430Ser Multiple submitters congenital myasthenic syndrome ⚠
  • c.1195+1G>T Single submitter congenital myasthenic syndrome 5
  • c.1195+2T>C Single submitter congenital myasthenic syndrome 5
  • c.1195+2T>G Single submitter congenital myasthenic syndrome 5
  • c.188_321del Single submitter Synaptic congenital myasthenic syndromes
  • c.394-1G>A Single submitter congenital myasthenic syndrome 5
  • p.Arg236Ter Single submitter congenital myasthenic syndrome 5
  • p.Asn335fs Single submitter congenital myasthenic syndrome 5
  • p.Cys405fs Single submitter congenital myasthenic syndrome 5
  • p.Cys427Ter Single submitter congenital myasthenic syndrome 5
  • p.Cys52Ter Single submitter congenital myasthenic syndrome 5
  • p.Cys93Ter Single submitter Abnormality of the musculature
  • p.Gln371Ter Single submitter congenital myasthenic syndrome 5
  • p.Gln95Ter Single submitter
  • p.Glu121Ter Single submitter congenital myasthenic syndrome 5
  • p.Glu124Ter Single submitter congenital myasthenic syndrome 5
  • p.Gly228Ter Single submitter congenital myasthenic syndrome 5
  • p.Gly240Ter Single submitter congenital myasthenic syndrome 5
  • p.Gly267fs Single submitter congenital myasthenic syndrome 5
  • p.Gly272Glu Single submitter Synaptic congenital myasthenic syndromes ⚠
  • p.Gly283Ter Single submitter congenital myasthenic syndrome 5
  • p.Gly289Ter Single submitter congenital myasthenic syndrome 5
  • p.Gly394fs Single submitter congenital myasthenic syndrome 5
  • p.Gly436fs Single submitter congenital myasthenic syndrome 5
  • p.Ile275fs Single submitter congenital myasthenic syndrome 5
  • p.Leu37fs Single submitter congenital myasthenic syndrome 5
  • p.Leu40fs Single submitter congenital myasthenic syndrome 5
  • p.Leu9fs Single submitter congenital myasthenic syndrome 5
  • p.Pro59Gln Single submitter congenital myasthenic syndrome 5 ⚠
  • p.Ser257fs Single submitter congenital myasthenic syndrome 5
  • p.Ser313fs Single submitter
  • p.Trp354Ter Single submitter congenital myasthenic syndrome 5
  • c.107_321del No assertion criteria congenital myasthenic syndrome 5
  • c.(814+1_815-1 No assertion criteria congenital myasthenic syndrome 5
  • p.Arg399His No assertion criteria congenital myasthenic syndrome 5 ⚠
  • p.Thr426Ile No assertion criteria congenital myasthenic syndrome 5

Pathogenic/Likely pathogenic 16

  • c.220-1G>A Multiple submitters congenital myasthenic syndrome 5
  • c.529-2A>G Multiple submitters congenital myasthenic syndrome 5
  • c.954+1G>A Multiple submitters congenital myasthenic syndrome 5
  • c.955-2A>C Multiple submitters congenital myasthenic syndrome 5
  • c.955-2A>T Multiple submitters congenital myasthenic syndrome 5
  • p.Arg127Ter Multiple submitters congenital myasthenic syndrome 5
  • p.Arg410Trp Multiple submitters congenital myasthenic syndrome ⚠
  • p.Asp342Glu Multiple submitters Synaptic congenital myasthenic syndromes
  • p.Asp377fs Multiple submitters congenital myasthenic syndrome 5
  • p.Cys427= Multiple submitters Synaptic congenital myasthenic syndromes
  • p.His409fs Multiple submitters congenital myasthenic syndrome 5
  • p.Ile20fs Multiple submitters congenital myasthenic syndrome 5
  • p.Leu331fs Multiple submitters congenital myasthenic syndrome
  • p.Met276fs Multiple submitters Synaptic congenital myasthenic syndromes
  • p.Pro59Ser Multiple submitters congenital myasthenic syndrome 5 ⚠
  • p.Trp148Ter Multiple submitters congenital myasthenic syndrome 5

Likely pathogenic 46

  • c.106+2_106+10del Multiple submitters congenital myasthenic syndrome 5
  • c.555+1G>A Multiple submitters congenital myasthenic syndrome 5
  • c.718-1276C>T Multiple submitters congenital myasthenic syndrome 5
  • c.814+2T>C Multiple submitters congenital myasthenic syndrome 5
  • c.107-1G>A Single submitter congenital myasthenic syndrome 5
  • c.1196-2A>G Single submitter congenital myasthenic syndrome 5
  • c.322-1G>C Single submitter congenital myasthenic syndrome 5
  • c.366+1G>C Single submitter congenital myasthenic syndrome 5
  • c.366+1G>T Single submitter congenital myasthenic syndrome 5
  • c.465+1_465+10del Single submitter congenital myasthenic syndrome 5
  • c.466-1G>A Single submitter congenital myasthenic syndrome 5
  • c.528+1G>A Single submitter congenital myasthenic syndrome 5
  • c.718-1G>A Single submitter congenital myasthenic syndrome 5
  • c.718-1G>T Single submitter congenital myasthenic syndrome 5
  • c.814+1G>A Single submitter congenital myasthenic syndrome 5
  • c.955-1G>C Single submitter congenital myasthenic syndrome 5
  • p.Arg71Ter Single submitter Abnormality of the musculature
  • p.Asp447Val Single submitter congenital myasthenic syndrome 5
  • p.Cys291fs Single submitter congenital myasthenic syndrome
  • p.Cys417Tyr Single submitter congenital myasthenic syndrome 5
  • p.Cys427Arg Single submitter
  • p.Cys444Tyr Single submitter congenital myasthenic syndrome 5
  • p.Gln107fs Single submitter congenital myasthenic syndrome 5
  • p.Gln107Ter Single submitter congenital myasthenic syndrome 5
  • p.Gln14Ter Single submitter congenital myasthenic syndrome 5
  • p.Gln42Ter Single submitter congenital myasthenic syndrome 5
  • p.Gln90Ter Single submitter congenital myasthenic syndrome 5
  • p.Glu415Gly Single submitter congenital myasthenic syndrome 5
  • p.Gly186Ter Single submitter congenital myasthenic syndrome 5
  • p.Gly406Ala Single submitter congenital myasthenic syndrome 5 ⚠
  • p.Gly433Glu Single submitter congenital myasthenic syndrome 5
  • p.Ile337Thr Single submitter
  • p.Leu352fs Single submitter congenital myasthenic syndrome 5
  • p.Lys197Ter Single submitter congenital myasthenic syndrome 5
  • p.Met83fs Single submitter congenital myasthenic syndrome 5
  • p.Phe284fs Single submitter congenital myasthenic syndrome 5
  • p.Phe67fs Single submitter congenital myasthenic syndrome 5
  • p.Pro32fs Single submitter congenital myasthenic syndrome 5
  • p.Pro6_Met7insTer Single submitter congenital myasthenic syndrome 5
  • p.Pro63fs Single submitter congenital myasthenic syndrome 5
  • p.Ser420fs Single submitter Abnormality of the musculature
  • p.Tyr304fs Single submitter Abnormality of the musculature
  • p.Tyr363Ter Single submitter Abnormality of the musculature
  • p.Val247fs Single submitter congenital myasthenic syndrome 5
  • p.Gly406Glu No assertion criteria congenital myasthenic syndrome
  • p.Gly413fs No assertion criteria congenital myasthenic syndrome

Conflicting classifications of pathogenicity 17

  • c.106+6T>C Single submitter congenital myasthenic syndrome 5
  • c.718-9C>T Single submitter congenital myasthenic syndrome 5
  • c.814+11C>T Single submitter congenital myasthenic syndrome 5
  • p.Ala369Val Single submitter Inborn genetic diseases ⚠
  • p.Arg340His Single submitter congenital myasthenic syndrome 5 ⚠
  • p.Arg452Cys Single submitter congenital myasthenic syndrome ⚠
  • p.Gly114= Single submitter congenital myasthenic syndrome 5
  • p.Gly174= Single submitter congenital myasthenic syndrome 5
  • p.Gly373Ser Single submitter Inborn genetic diseases ⚠
  • p.Met7Val Single submitter congenital myasthenic syndrome 5 ⚠
  • p.Pro314= Single submitter congenital myasthenic syndrome 5
  • p.Pro450= Single submitter congenital myasthenic syndrome 5
  • p.Pro56Leu Single submitter Inborn genetic diseases ⚠
  • p.Ser187= Single submitter congenital myasthenic syndrome 5
  • p.Thr441Ala Single submitter congenital myasthenic syndrome 5 ⚠
  • p.Thr8Ser Single submitter congenital myasthenic syndrome 5 ⚠
  • p.Tyr304= Single submitter congenital myasthenic syndrome 5

Benign 66

Benign/Likely benign 6

  • c.107-19G>A Multiple submitters congenital myasthenic syndrome 5
  • c.393+11C>T Multiple submitters congenital myasthenic syndrome 5
  • p.Asp370Asn Multiple submitters congenital myasthenic syndrome 5
  • p.Pro263= Multiple submitters congenital myasthenic syndrome 5
  • p.Pro361Ser Multiple submitters congenital myasthenic syndrome 5 ⚠
  • p.Ser100= Multiple submitters congenital myasthenic syndrome 5

Likely benign 187

  • c.106+196G>A Multiple submitters
  • c.107-9263G>C Multiple submitters congenital myasthenic syndrome 5
  • c.1196-45C>T Multiple submitters
  • c.1299-31G>A Multiple submitters
  • c.321+208A>G Multiple submitters
  • c.367-140C>G Multiple submitters
  • c.367-50G>A Multiple submitters
  • c.393+268C>G Multiple submitters
  • c.393+37G>A Multiple submitters
  • c.394-34C>T Multiple submitters
  • c.466-165G>A Multiple submitters
  • c.528+131C>T Multiple submitters
  • c.600+52G>A Multiple submitters
  • c.718-11C>A Multiple submitters congenital myasthenic syndrome 5
  • c.815-5C>T Multiple submitters congenital myasthenic syndrome 5
  • p.Pro24= Multiple submitters congenital myasthenic syndrome 5
  • c.106+11G>A Single submitter congenital myasthenic syndrome 5
  • c.106+11G>T Single submitter congenital myasthenic syndrome 5
  • c.106+18C>G Single submitter congenital myasthenic syndrome 5
  • c.106+7G>C Single submitter congenital myasthenic syndrome 5
  • c.106+7G>T Single submitter congenital myasthenic syndrome 5
  • c.107-20C>G Single submitter congenital myasthenic syndrome 5
  • c.107-272G>A Single submitter
  • c.107-4dup Single submitter congenital myasthenic syndrome 5
  • c.1195+17C>A Single submitter congenital myasthenic syndrome 5
  • c.1195+17C>T Single submitter congenital myasthenic syndrome 5
  • c.1195+328G>A Single submitter
  • c.1196-15_1196-13del Single submitter congenital myasthenic syndrome 5
  • c.1196-16C>T Single submitter congenital myasthenic syndrome 5
  • c.1196-17T>A Single submitter congenital myasthenic syndrome 5
  • c.1196-19C>A Single submitter congenital myasthenic syndrome 5
  • c.1298+190G>A Single submitter
  • c.1298+19C>G Single submitter congenital myasthenic syndrome 5
  • c.1298+7A>T Single submitter congenital myasthenic syndrome 5
  • c.1299-15C>A Single submitter congenital myasthenic syndrome 5
  • c.1299-20C>T Single submitter congenital myasthenic syndrome 5
  • c.1299-5C>T Single submitter congenital myasthenic syndrome 5
  • c.1299-8T>C Single submitter congenital myasthenic syndrome 5
  • c.1299-8T>G Single submitter congenital myasthenic syndrome 5
  • c.1299-9C>T Single submitter congenital myasthenic syndrome 5
  • c.219+11T>C Single submitter congenital myasthenic syndrome 5
  • c.220-130G>A Single submitter
  • c.220-133G>C Single submitter
  • c.220-13C>T Single submitter congenital myasthenic syndrome 5
  • c.220-17G>C Single submitter congenital myasthenic syndrome 5
  • c.220-19G>A Single submitter congenital myasthenic syndrome 5
  • c.220-205T>C Single submitter
  • c.321+16C>T Single submitter congenital myasthenic syndrome 5
  • c.321+17G>A Single submitter congenital myasthenic syndrome 5
  • c.321+18G>C Single submitter congenital myasthenic syndrome 5
  • c.321+19A>T Single submitter congenital myasthenic syndrome 5
  • c.321+20C>A Single submitter congenital myasthenic syndrome 5
  • c.321+27C>T Single submitter
  • c.321+7G>A Single submitter congenital myasthenic syndrome 5
  • c.321+7G>T Single submitter congenital myasthenic syndrome 5
  • c.322-15A>G Single submitter congenital myasthenic syndrome 5
  • c.322-19T>C Single submitter congenital myasthenic syndrome 5
  • c.322-247C>T Single submitter
  • c.366+15T>C Single submitter congenital myasthenic syndrome 5
  • c.366+9C>T Single submitter congenital myasthenic syndrome 5
  • c.367-10C>T Single submitter congenital myasthenic syndrome 5
  • c.367-20C>T Single submitter congenital myasthenic syndrome 5
  • c.367-6C>T Single submitter congenital myasthenic syndrome 5
  • c.367-9C>T Single submitter
  • c.393+12G>A Single submitter congenital myasthenic syndrome 5
  • c.393+18C>T Single submitter congenital myasthenic syndrome 5
  • c.393+224_393+226del Single submitter
  • c.394-19T>C Single submitter congenital myasthenic syndrome 5
  • c.465+102C>T Single submitter
  • c.465+52A>G Single submitter
  • c.465+7G>T Single submitter congenital myasthenic syndrome 5
  • c.466-11A>G Single submitter congenital myasthenic syndrome 5
  • c.466-14T>C Single submitter congenital myasthenic syndrome 5
  • c.466-20TCT[2] Single submitter congenital myasthenic syndrome 5
  • c.466-4A>G Single submitter congenital myasthenic syndrome 5
  • c.466-5C>T Single submitter congenital myasthenic syndrome 5
  • c.528+15C>G Single submitter congenital myasthenic syndrome 5
  • c.528+17A>G Single submitter congenital myasthenic syndrome 5
  • c.528+18A>G Single submitter congenital myasthenic syndrome 5
  • c.528+19T>C Single submitter congenital myasthenic syndrome 5
  • c.529-17C>T Single submitter congenital myasthenic syndrome 5
  • c.529-18C>A Single submitter congenital myasthenic syndrome 5
  • c.529-18C>T Single submitter congenital myasthenic syndrome 5
  • c.529-3T>C Single submitter congenital myasthenic syndrome 5
  • c.529-4T>G Single submitter congenital myasthenic syndrome 5
  • c.555+16G>C Single submitter congenital myasthenic syndrome 5
  • c.555+31G>A Single submitter
  • c.555+7G>A Single submitter congenital myasthenic syndrome 5
  • c.556-15A>T Single submitter congenital myasthenic syndrome 5
  • c.556-7T>C Single submitter congenital myasthenic syndrome 5
  • c.600+15C>T Single submitter congenital myasthenic syndrome 5
  • c.600+18T>C Single submitter congenital myasthenic syndrome 5
  • c.600+22T>C Single submitter
  • c.601-12C>T Single submitter congenital myasthenic syndrome 5
  • c.601-16G>A Single submitter congenital myasthenic syndrome 5
  • c.601-18T>C Single submitter congenital myasthenic syndrome 5
  • c.601-20A>G Single submitter congenital myasthenic syndrome 5
  • c.636+8A>G Single submitter congenital myasthenic syndrome 5
  • c.636+9C>A Single submitter congenital myasthenic syndrome 5
  • c.637-11C>T Single submitter congenital myasthenic syndrome 5
  • c.637-13T>C Single submitter congenital myasthenic syndrome 5
  • c.637-19T>A Single submitter congenital myasthenic syndrome 5
  • c.637-5T>C Single submitter
  • c.717+16C>A Single submitter congenital myasthenic syndrome 5
  • c.717+26G>A Single submitter
  • c.717+9C>T Single submitter congenital myasthenic syndrome 5
  • c.718-1179C>T Single submitter
  • c.718-14T>C Single submitter congenital myasthenic syndrome 5
  • c.718-17G>A Single submitter congenital myasthenic syndrome 5
  • c.718-5G>A Single submitter congenital myasthenic syndrome 5
  • c.814+12A>G Single submitter congenital myasthenic syndrome 5
  • c.814+12dup Single submitter congenital myasthenic syndrome 5
  • c.814+13C>T Single submitter congenital myasthenic syndrome 5
  • c.815-1064del Single submitter congenital myasthenic syndrome 5
  • c.815-16G>A Single submitter congenital myasthenic syndrome 5
  • c.815-243C>T Single submitter
  • c.955-18C>T Single submitter congenital myasthenic syndrome 5
  • c.955-6T>C Single submitter congenital myasthenic syndrome 5
  • c.955-7C>G Single submitter congenital myasthenic syndrome 5
  • c.955-9C>T Single submitter congenital myasthenic syndrome 5
  • p.Ala403= Single submitter congenital myasthenic syndrome 5
  • p.Arg410= Single submitter
  • p.Arg45= Single submitter congenital myasthenic syndrome 5
  • p.Asn335= Single submitter congenital myasthenic syndrome 5
  • p.Asp244= Single submitter
  • p.Asp387= Single submitter congenital myasthenic syndrome 5
  • p.Asp388= Single submitter congenital myasthenic syndrome 5
  • p.Asp395= Single submitter congenital myasthenic syndrome 5
  • p.Asp407= Single submitter congenital myasthenic syndrome 5
  • p.Asp418= Single submitter congenital myasthenic syndrome 5
  • p.Cys400= Single submitter congenital myasthenic syndrome 5
  • p.Cys52= Single submitter congenital myasthenic syndrome 5
  • p.Gln371= Single submitter congenital myasthenic syndrome 5
  • p.Gln439= Single submitter congenital myasthenic syndrome 5
  • p.Glu384= Single submitter congenital myasthenic syndrome 5
  • p.Gly135= Single submitter congenital myasthenic syndrome 5
  • p.Gly144= Single submitter congenital myasthenic syndrome 5
  • p.Gly150= Single submitter congenital myasthenic syndrome 5
  • p.Gly186= Single submitter congenital myasthenic syndrome 5
  • p.Gly207= Single submitter congenital myasthenic syndrome 5
  • p.Gly234= Single submitter congenital myasthenic syndrome 5
  • p.Gly237= Single submitter congenital myasthenic syndrome 5
  • p.Gly243= Single submitter congenital myasthenic syndrome 5
  • p.Gly261= Single submitter congenital myasthenic syndrome 5
  • p.Gly264= Single submitter congenital myasthenic syndrome 5
  • p.Gly286= Single submitter congenital myasthenic syndrome 5
  • p.Gly408= Single submitter congenital myasthenic syndrome 5
  • p.Gly419= Single submitter congenital myasthenic syndrome 5
  • p.Gly433= Single submitter congenital myasthenic syndrome 5
  • p.Gly47= Single submitter congenital myasthenic syndrome 5
  • p.His372= Single submitter congenital myasthenic syndrome 5
  • p.Ile20= Single submitter congenital myasthenic syndrome 5
  • p.Ile446= Single submitter congenital myasthenic syndrome 5
  • p.Leu18= Single submitter congenital myasthenic syndrome 5
  • p.Leu40= Single submitter congenital myasthenic syndrome 5
  • p.Leu53= Single submitter congenital myasthenic syndrome 5
  • p.Leu82= Single submitter congenital myasthenic syndrome 5
  • p.Leu9= Single submitter congenital myasthenic syndrome 5
  • p.Leu98= Single submitter congenital myasthenic syndrome 5
  • p.Lys119= Single submitter congenital myasthenic syndrome 5
  • p.Lys218= Single submitter congenital myasthenic syndrome 5
  • p.Lys253= Single submitter congenital myasthenic syndrome 5
  • p.Phe339= Single submitter congenital myasthenic syndrome 5
  • p.Pro134= Single submitter congenital myasthenic syndrome 5
  • p.Pro136= Single submitter congenital myasthenic syndrome 5
  • p.Pro140= Single submitter congenital myasthenic syndrome 5
  • p.Pro143= Single submitter congenital myasthenic syndrome 5
  • p.Pro154= Single submitter congenital myasthenic syndrome 5
  • p.Pro256= Single submitter congenital myasthenic syndrome 5
  • p.Pro266= Single submitter congenital myasthenic syndrome 5
  • p.Pro268= Single submitter congenital myasthenic syndrome 5
  • p.Pro270= Single submitter congenital myasthenic syndrome 5
  • p.Pro285= Single submitter congenital myasthenic syndrome 5
  • p.Pro56= Single submitter congenital myasthenic syndrome 5
  • p.Pro60= Single submitter congenital myasthenic syndrome 5
  • p.Pro92= Single submitter congenital myasthenic syndrome 5
  • p.Ser29= Single submitter congenital myasthenic syndrome 5
  • p.Ser97= Single submitter
  • p.Thr116= Single submitter congenital myasthenic syndrome 5
  • p.Thr333= Single submitter congenital myasthenic syndrome 5
  • p.Thr426= Single submitter congenital myasthenic syndrome 5
  • p.Thr441= Single submitter congenital myasthenic syndrome 5
  • p.Thr449= Single submitter congenital myasthenic syndrome 5
  • p.Thr55= Single submitter congenital myasthenic syndrome 5
  • p.Tyr363= Single submitter congenital myasthenic syndrome 5
  • p.Tyr435= Single submitter congenital myasthenic syndrome 5
  • p.Val308= Single submitter congenital myasthenic syndrome 5

Uncertain significance 239