COG2 — 278 ClinVar variants

All ClinVar germline COG2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 122 flagged for review →

4 Pathogenic · 3 Likely pathogenic · 4 Conflicting · 50 Benign · 3 Benign/Likely benign · 92 Likely benign · 122 Uncertain significance

Full COG2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 122

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 3

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

Predictors lean, ClinVar uncertain 70

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

Predictors split 49

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

All COG2 variants

Pathogenic 4

  • p.Gln87fs Single submitter congenital disorder of glycosylation, type IIq
  • p.Ile146fs Single submitter congenital disorder of glycosylation, type IIq
  • p.Lys503fs Single submitter congenital disorder of glycosylation, type IIq
  • p.Thr175fs Single submitter congenital disorder of glycosylation, type IIq

Likely pathogenic 3

Conflicting classifications of pathogenicity 4

  • p.Ala676Thr Single submitter congenital disorder of glycosylation, type IIq ⚠
  • p.Asn73Ser Single submitter congenital disorder of glycosylation, type IIq ⚠
  • p.Ile134Met Single submitter congenital disorder of glycosylation, type IIq ⚠
  • p.Lys522Arg Single submitter congenital disorder of glycosylation, type IIq ⚠

Benign 50

Benign/Likely benign 3

  • p.Asp338= Multiple submitters congenital disorder of glycosylation, type IIq
  • p.Thr236= Multiple submitters congenital disorder of glycosylation, type IIq
  • p.Val589Ile Multiple submitters congenital disorder of glycosylation, type IIq

Likely benign 92

  • c.2115+18G>A Multiple submitters congenital disorder of glycosylation, type IIq
  • c.2115+277A>G Multiple submitters
  • c.301-79G>A Multiple submitters
  • p.Arg510Cys Multiple submitters congenital disorder of glycosylation, type IIq
  • p.Asp687= Multiple submitters congenital disorder of glycosylation, type IIq
  • p.Gln209= Multiple submitters congenital disorder of glycosylation, type IIq
  • p.Thr511Ser Multiple submitters congenital disorder of glycosylation, type IIq
  • p.Val653Ile Multiple submitters congenital disorder of glycosylation, type IIq ⚠
  • c.1026+10C>T Single submitter congenital disorder of glycosylation, type IIq
  • c.1026+11G>A Single submitter congenital disorder of glycosylation, type IIq
  • c.1026+14C>T Single submitter congenital disorder of glycosylation, type IIq
  • c.1026+17C>T Single submitter
  • c.1026+18G>A Single submitter congenital disorder of glycosylation, type IIq
  • c.1166+18C>T Single submitter congenital disorder of glycosylation, type IIq
  • c.1166+19G>A Single submitter congenital disorder of glycosylation, type IIq
  • c.1167-19C>A Single submitter congenital disorder of glycosylation, type IIq
  • c.1381-10C>T Single submitter congenital disorder of glycosylation, type IIq
  • c.1578+11G>C Single submitter congenital disorder of glycosylation, type IIq
  • c.1579-13A>G Single submitter congenital disorder of glycosylation, type IIq
  • c.1935-17C>T Single submitter congenital disorder of glycosylation, type IIq
  • c.2115+14C>T Single submitter congenital disorder of glycosylation, type IIq
  • c.2115+15G>A Single submitter congenital disorder of glycosylation, type IIq
  • c.2115+7C>T Single submitter congenital disorder of glycosylation, type IIq
  • c.2116-10G>A Single submitter
  • c.2116-59T>C Single submitter
  • c.2116-72T>G Single submitter
  • c.235-8del Single submitter congenital disorder of glycosylation, type IIq
  • c.300+11C>T Single submitter congenital disorder of glycosylation, type IIq
  • c.300+12G>A Single submitter congenital disorder of glycosylation, type IIq
  • c.301-10T>G Single submitter
  • c.301-11G>T Single submitter congenital disorder of glycosylation, type IIq
  • c.301-9C>T Single submitter congenital disorder of glycosylation, type IIq
  • c.381+4T>C Single submitter congenital disorder of glycosylation, type IIq
  • c.381+8C>T Single submitter congenital disorder of glycosylation, type IIq
  • c.485+19A>G Single submitter congenital disorder of glycosylation, type IIq
  • c.485+8T>A Single submitter congenital disorder of glycosylation, type IIq
  • c.594+10G>A Single submitter congenital disorder of glycosylation, type IIq
  • c.72+20C>T Single submitter congenital disorder of glycosylation, type IIq
  • c.73-10T>C Single submitter
  • c.73-19C>T Single submitter congenital disorder of glycosylation, type IIq
  • c.774+9A>G Single submitter
  • c.899+15C>G Single submitter congenital disorder of glycosylation, type IIq
  • c.900-19A>T Single submitter congenital disorder of glycosylation, type IIq
  • c.900-20T>C Single submitter congenital disorder of glycosylation, type IIq
  • p.Ala205= Single submitter congenital disorder of glycosylation, type IIq
  • p.Ala369= Single submitter congenital disorder of glycosylation, type IIq
  • p.Ala394= Single submitter congenital disorder of glycosylation, type IIq
  • p.Ala713= Single submitter
  • p.Ala723Thr Single submitter
  • p.Arg124= Single submitter congenital disorder of glycosylation, type IIq
  • p.Arg464= Single submitter congenital disorder of glycosylation, type IIq
  • p.Asn381= Single submitter
  • p.Asn459Ser Single submitter
  • p.Asn655= Single submitter congenital disorder of glycosylation, type IIq
  • p.Cys129= Single submitter congenital disorder of glycosylation, type IIq
  • p.Gln135= Single submitter congenital disorder of glycosylation, type IIq
  • p.Gln489= Single submitter congenital disorder of glycosylation, type IIq
  • p.Glu281= Single submitter congenital disorder of glycosylation, type IIq
  • p.Glu433= Single submitter
  • p.Glu44= Single submitter
  • p.Glu469= Single submitter congenital disorder of glycosylation, type IIq
  • p.Glu704Lys Single submitter congenital disorder of glycosylation, type IIq
  • p.Gly218= Single submitter congenital disorder of glycosylation, type IIq
  • p.Gly637= Single submitter congenital disorder of glycosylation, type IIq
  • p.Leu180= Single submitter congenital disorder of glycosylation, type IIq
  • p.Leu214= Single submitter
  • p.Leu397= Single submitter congenital disorder of glycosylation, type IIq
  • p.Leu443= Single submitter congenital disorder of glycosylation, type IIq
  • p.Leu49= Single submitter congenital disorder of glycosylation, type IIq
  • p.Leu587= Single submitter congenital disorder of glycosylation, type IIq
  • p.Leu63= Single submitter congenital disorder of glycosylation, type IIq
  • p.Lys145= Single submitter congenital disorder of glycosylation, type IIq
  • p.Lys659= Single submitter congenital disorder of glycosylation, type IIq
  • p.Phe282= Single submitter congenital disorder of glycosylation, type IIq
  • p.Phe580= Single submitter congenital disorder of glycosylation, type IIq
  • p.Pro12= Single submitter congenital disorder of glycosylation, type IIq
  • p.Pro163= Single submitter congenital disorder of glycosylation, type IIq
  • p.Pro329= Single submitter congenital disorder of glycosylation, type IIq
  • p.Pro334= Single submitter congenital disorder of glycosylation, type IIq
  • p.Pro337= Single submitter congenital disorder of glycosylation, type IIq
  • p.Pro678= Single submitter congenital disorder of glycosylation, type IIq
  • p.Ser330= Single submitter
  • p.Ser363= Single submitter
  • p.Ser4= Single submitter congenital disorder of glycosylation, type IIq
  • p.Ser431= Single submitter congenital disorder of glycosylation, type IIq
  • p.Ser585= Single submitter congenital disorder of glycosylation, type IIq
  • p.Ser686= Single submitter congenital disorder of glycosylation, type IIq
  • p.Thr14= Single submitter congenital disorder of glycosylation, type IIq
  • p.Thr345= Single submitter
  • p.Thr58= Single submitter congenital disorder of glycosylation, type IIq
  • p.Tyr234= Single submitter congenital disorder of glycosylation, type IIq
  • p.Val600= Single submitter congenital disorder of glycosylation, type IIq

Uncertain significance 122