CNTN1 — 711 ClinVar variants

All ClinVar germline CNTN1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 273 flagged for review →

16 Pathogenic · 1 Pathogenic/Likely pathogenic · 6 Likely pathogenic · 12 Conflicting · 70 Benign · 12 Benign/Likely benign · 313 Likely benign · 281 Uncertain significance

Full CNTN1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 273

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 4

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

Predictors lean, ClinVar uncertain 150

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

Predictors split 119

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

All CNTN1 variants

Pathogenic 16

  • p.Arg571Ter Single submitter Compton-North congenital myopathy
  • p.Arg90Ter Single submitter Compton-North congenital myopathy
  • p.Gln247Ter Single submitter Compton-North congenital myopathy
  • p.Glu21fs Single submitter Compton-North congenital myopathy
  • p.Glu838Ter Single submitter Compton-North congenital myopathy
  • p.Glu975Ter Single submitter Compton-North congenital myopathy
  • p.Ile359fs Single submitter Compton-North congenital myopathy
  • p.Lys835_Ile836insTer Single submitter Compton-North congenital myopathy
  • p.Phe878fs Single submitter Compton-North congenital myopathy
  • p.Ser932Ter Single submitter Compton-North congenital myopathy
  • p.Thr758fs Single submitter Compton-North congenital myopathy
  • p.Trp454Ter Single submitter Compton-North congenital myopathy
  • p.Tyr162fs Single submitter Compton-North congenital myopathy
  • p.Val539fs Single submitter Compton-North congenital myopathy
  • p.Val74fs Single submitter Compton-North congenital myopathy
  • p.Ser291fs No assertion criteria Compton-North congenital myopathy

Pathogenic/Likely pathogenic 1

  • p.Gly491fs Multiple submitters Compton-North congenital myopathy

Likely pathogenic 6

Conflicting classifications of pathogenicity 12

Benign 70

Benign/Likely benign 12

  • c.1507+19G>T Multiple submitters Compton-North congenital myopathy
  • c.401-14del Multiple submitters Compton-North congenital myopathy
  • c.497-17G>T Multiple submitters Compton-North congenital myopathy
  • p.Ala69= Multiple submitters Compton-North congenital myopathy
  • p.Ala866= Multiple submitters Compton-North congenital myopathy
  • p.Arg977Cys Multiple submitters Compton-North congenital myopathy ⚠
  • p.Asn521= Multiple submitters Compton-North congenital myopathy
  • p.Cys18= Multiple submitters Compton-North congenital myopathy
  • p.Gly467= Multiple submitters Compton-North congenital myopathy
  • p.His831= Multiple submitters Compton-North congenital myopathy
  • p.Ser291= Multiple submitters Compton-North congenital myopathy
  • p.Tyr637= Multiple submitters Compton-North congenital myopathy

Likely benign 313

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

  • c.1229-85G>A Multiple submitters
  • c.1229-92C>T Multiple submitters
  • c.1963+96A>G Multiple submitters
  • c.2114-17T>G Multiple submitters Compton-North congenital myopathy
  • c.2114-20T>C Multiple submitters Compton-North congenital myopathy
  • c.227+69C>T Multiple submitters
  • c.2523+4C>T Multiple submitters Compton-North congenital myopathy
  • c.2823+58A>G Multiple submitters
  • c.2823+5A>G Multiple submitters Compton-North congenital myopathy
  • c.2824-6T>C Multiple submitters Compton-North congenital myopathy
  • c.400+13T>C Multiple submitters Compton-North congenital myopathy
  • c.61+56G>A Multiple submitters
  • c.61+79A>C Multiple submitters
  • c.62-189C>T Multiple submitters
  • c.804-8A>G Multiple submitters Compton-North congenital myopathy
  • c.*210A>G Multiple submitters
  • p.Ala898= Multiple submitters Compton-North congenital myopathy
  • p.Asn395= Multiple submitters Compton-North congenital myopathy
  • p.Asn49= Multiple submitters Compton-North congenital myopathy
  • p.Cys114= Multiple submitters Compton-North congenital myopathy
  • p.Gln574= Multiple submitters Compton-North congenital myopathy
  • p.Glu851= Multiple submitters Compton-North congenital myopathy
  • p.His828= Multiple submitters Inborn genetic diseases
  • p.Leu302Pro Multiple submitters Compton-North congenital myopathy
  • p.Leu868= Multiple submitters Compton-North congenital myopathy
  • p.Met417Ile Multiple submitters Compton-North congenital myopathy
  • p.Ser625= Multiple submitters Compton-North congenital myopathy
  • p.Thr285= Multiple submitters Compton-North congenital myopathy
  • p.Tyr972= Multiple submitters Compton-North congenital myopathy
  • p.Val976= Multiple submitters Compton-North congenital myopathy
  • c.1110+15G>A Single submitter Compton-North congenital myopathy
  • c.1110+16T>G Single submitter Compton-North congenital myopathy
  • c.1110+18C>A Single submitter Compton-North congenital myopathy
  • c.1111-202G>A Single submitter
  • c.1111-7T>C Single submitter Compton-North congenital myopathy
  • c.1228+10A>G Single submitter Compton-North congenital myopathy
  • c.1228+249T>C Single submitter
  • c.1228+8T>C Single submitter Compton-North congenital myopathy
  • c.1229-113G>A Single submitter
  • c.1229-19C>A Single submitter Compton-North congenital myopathy
  • c.1229-204T>C Single submitter
  • c.1229-8del Single submitter Compton-North congenital myopathy
  • c.1379+16A>C Single submitter Compton-North congenital myopathy
  • c.1380-149C>T Single submitter
  • c.1380-14T>G Single submitter Compton-North congenital myopathy
  • c.1380-18A>G Single submitter Compton-North congenital myopathy
  • c.1380-326G>A Single submitter
  • c.1507+10T>C Single submitter Compton-North congenital myopathy
  • c.1507+15G>T Single submitter Compton-North congenital myopathy
  • c.1507+17G>A Single submitter Compton-North congenital myopathy
  • c.1508-13del Single submitter Compton-North congenital myopathy
  • c.1508-16A>G Single submitter Compton-North congenital myopathy
  • c.1508-4A>G Single submitter Compton-North congenital myopathy
  • c.1508-5T>C Single submitter Compton-North congenital myopathy
  • c.1508-6A>G Single submitter Compton-North congenital myopathy
  • c.1804+13A>C Single submitter Compton-North congenital myopathy
  • c.1804+16T>A Single submitter Compton-North congenital myopathy
  • c.1804+321T>A Single submitter
  • c.1804+7G>A Single submitter Compton-North congenital myopathy
  • c.1804+7G>C Single submitter Compton-North congenital myopathy
  • c.1805-17C>T Single submitter Compton-North congenital myopathy
  • c.1963+10_1963+13del Single submitter Compton-North congenital myopathy
  • c.1964-15A>C Single submitter Compton-North congenital myopathy
  • c.1964-17C>A Single submitter Compton-North congenital myopathy
  • c.2113+294del Single submitter
  • c.2113+309_2113+312del Single submitter
  • c.2113+7A>G Single submitter Compton-North congenital myopathy
  • c.2114-15del Single submitter Compton-North congenital myopathy
  • c.2114-17T>A Single submitter Compton-North congenital myopathy
  • c.2114-19A>G Single submitter Compton-North congenital myopathy
  • c.2184+10G>A Single submitter Compton-North congenital myopathy
  • c.2184+15G>C Single submitter Compton-North congenital myopathy
  • c.2184+217G>A Single submitter
  • c.2185-11T>C Single submitter
  • c.2185-344G>C Single submitter
  • c.2185-6A>G Single submitter Compton-North congenital myopathy
  • c.227+10C>T Single submitter Compton-North congenital myopathy
  • c.227+12C>T Single submitter Compton-North congenital myopathy
  • c.227+13G>A Single submitter Compton-North congenital myopathy
  • c.227+20T>C Single submitter Compton-North congenital myopathy
  • c.228-5C>A Single submitter Compton-North congenital myopathy
  • c.228-5C>T Single submitter Compton-North congenital myopathy
  • c.2419+21_2419+23del Single submitter Compton-North congenital myopathy
  • c.2420-13C>T Single submitter Compton-North congenital myopathy
  • c.2420-16del Single submitter Compton-North congenital myopathy
  • c.2420-328del Single submitter
  • c.2523+12T>C Single submitter Compton-North congenital myopathy
  • c.2523+257C>T Single submitter
  • c.2523+51C>T Single submitter
  • c.2524-10A>G Single submitter Compton-North congenital myopathy
  • c.2524-11A>T Single submitter Compton-North congenital myopathy
  • c.2524-162T>G Single submitter
  • c.2524-16T>C Single submitter Compton-North congenital myopathy
  • c.2524-19T>A Single submitter Compton-North congenital myopathy
  • c.2524-20C>T Single submitter Compton-North congenital myopathy
  • c.2524-6T>C Single submitter Compton-North congenital myopathy
  • c.2524-9T>C Single submitter Compton-North congenital myopathy
  • c.2710+12G>A Single submitter Compton-North congenital myopathy
  • c.2710+20T>C Single submitter Compton-North congenital myopathy
  • c.2710+296A>G Single submitter
  • c.2711-11A>G Single submitter Compton-North congenital myopathy
  • c.2711-19A>G Single submitter Compton-North congenital myopathy
  • c.2823+184T>C Single submitter
  • c.2823+189A>T Single submitter
  • c.2823+18T>A Single submitter Compton-North congenital myopathy
  • c.2823+18T>C Single submitter Compton-North congenital myopathy
  • c.2823+244G>A Single submitter
  • c.2823+56C>G Single submitter
  • c.2824-15T>A Single submitter Compton-North congenital myopathy
  • c.2980+7G>A Single submitter Compton-North congenital myopathy
  • c.2981-12T>C Single submitter Compton-North congenital myopathy
  • c.2981-18T>C Single submitter Compton-North congenital myopathy
  • c.400+287G>C Single submitter
  • c.400+8A>C Single submitter Compton-North congenital myopathy
  • c.400+8A>G Single submitter Compton-North congenital myopathy
  • c.401-17T>G Single submitter Compton-North congenital myopathy
  • c.401-6A>G Single submitter Compton-North congenital myopathy
  • c.401-8G>A Single submitter Compton-North congenital myopathy
  • c.401-8G>T Single submitter
  • c.401-9C>G Single submitter Compton-North congenital myopathy
  • c.496+181G>A Single submitter
  • c.496+18C>G Single submitter Compton-North congenital myopathy
  • c.496+20_496+23del Single submitter Compton-North congenital myopathy
  • c.496+230AT[21] Single submitter
  • c.497-112C>T Single submitter
  • c.497-16C>T Single submitter Compton-North congenital myopathy
  • c.497-19A>T Single submitter Compton-North congenital myopathy
  • c.497-267C>G Single submitter
  • c.497-4C>T Single submitter Compton-North congenital myopathy
  • c.61+11T>G Single submitter Compton-North congenital myopathy
  • c.61+12C>A Single submitter Compton-North congenital myopathy
  • c.61+16T>C Single submitter Compton-North congenital myopathy
  • c.61+74G>A Single submitter
  • c.62-15T>C Single submitter Compton-North congenital myopathy
  • c.62-7T>A Single submitter Compton-North congenital myopathy
  • c.703+15T>G Single submitter Compton-North congenital myopathy
  • c.703+17T>A Single submitter Compton-North congenital myopathy
  • c.704-11C>G Single submitter Compton-North congenital myopathy
  • c.803+14C>T Single submitter Compton-North congenital myopathy
  • c.803+15A>G Single submitter Compton-North congenital myopathy
  • c.803+7A>G Single submitter Compton-North congenital myopathy
  • c.803+9A>T Single submitter Compton-North congenital myopathy
  • c.804-13C>G Single submitter Compton-North congenital myopathy
  • c.804-17G>C Single submitter Compton-North congenital myopathy
  • c.804-19T>C Single submitter Compton-North congenital myopathy
  • c.804-20C>T Single submitter Compton-North congenital myopathy
  • c.804-7T>C Single submitter Compton-North congenital myopathy
  • c.94+10C>T Single submitter Compton-North congenital myopathy
  • c.94+15G>C Single submitter Compton-North congenital myopathy
  • c.94+19A>G Single submitter Compton-North congenital myopathy
  • c.95-5T>C Single submitter Compton-North congenital myopathy
  • c.95-7C>A Single submitter Compton-North congenital myopathy
  • c.985+20T>A Single submitter
  • c.985+211G>C Single submitter
  • c.985+8del Single submitter Compton-North congenital myopathy
  • c.986-16G>A Single submitter Compton-North congenital myopathy
  • c.986-16G>C Single submitter Compton-North congenital myopathy
  • c.-76-325T>G Single submitter
  • p.Ala116= Single submitter Compton-North congenital myopathy
  • p.Ala242= Single submitter Compton-North congenital myopathy
  • p.Ala286= Single submitter Compton-North congenital myopathy
  • p.Ala386= Single submitter Compton-North congenital myopathy
  • p.Ala399= Single submitter Compton-North congenital myopathy
  • p.Ala410= Single submitter Compton-North congenital myopathy
  • p.Ala427= Single submitter Compton-North congenital myopathy
  • p.Ala441= Single submitter Compton-North congenital myopathy
  • p.Ala514= Single submitter Compton-North congenital myopathy
  • p.Ala522= Single submitter Compton-North congenital myopathy
  • p.Ala528= Single submitter Compton-North congenital myopathy
  • p.Ala573= Single submitter Compton-North congenital myopathy
  • p.Ala67= Single submitter Compton-North congenital myopathy
  • p.Ala705= Single submitter Compton-North congenital myopathy
  • p.Ala978= Single submitter Compton-North congenital myopathy
  • p.Arg143= Single submitter Compton-North congenital myopathy
  • p.Arg147= Single submitter Compton-North congenital myopathy
  • p.Arg186= Single submitter Compton-North congenital myopathy
  • p.Arg274= Single submitter Compton-North congenital myopathy
  • p.Arg316= Single submitter Compton-North congenital myopathy
  • p.Arg506= Single submitter Compton-North congenital myopathy
  • p.Arg698Lys Single submitter Inborn genetic diseases
  • p.Arg721= Single submitter Compton-North congenital myopathy
  • p.Arg90= Single submitter Compton-North congenital myopathy
  • p.Arg910= Single submitter Compton-North congenital myopathy
  • p.Arg977= Single submitter Compton-North congenital myopathy
  • p.Asn314= Single submitter Compton-North congenital myopathy
  • p.Asn338Ser Single submitter Compton-North congenital myopathy
  • p.Asn543= Single submitter Compton-North congenital myopathy
  • p.Asn685= Single submitter Compton-North congenital myopathy
  • p.Asn789= Single submitter Compton-North congenital myopathy
  • p.Asp250= Single submitter Compton-North congenital myopathy
  • p.Asp319= Single submitter Compton-North congenital myopathy
  • p.Asp347= Single submitter Compton-North congenital myopathy
  • p.Asp466= Single submitter Compton-North congenital myopathy
  • p.Asp614= Single submitter Compton-North congenital myopathy
  • p.Asp702= Single submitter Compton-North congenital myopathy
  • p.Asp83= Single submitter Compton-North congenital myopathy
  • p.Asp894= Single submitter Compton-North congenital myopathy
  • p.Asp951= Single submitter Compton-North congenital myopathy
  • p.Gln191= Single submitter Compton-North congenital myopathy
  • p.Gln46= Single submitter Compton-North congenital myopathy
  • p.Gln907= Single submitter Compton-North congenital myopathy
  • p.Glu44= Single submitter Compton-North congenital myopathy
  • p.Glu552= Single submitter Compton-North congenital myopathy
  • p.Gly110= Single submitter Compton-North congenital myopathy
  • p.Gly207= Single submitter Compton-North congenital myopathy
  • p.Gly306= Single submitter Compton-North congenital myopathy
  • p.Gly374= Single submitter Compton-North congenital myopathy
  • p.Gly497= Single submitter Compton-North congenital myopathy
  • p.Gly609= Single submitter Compton-North congenital myopathy
  • p.Gly717= Single submitter Compton-North congenital myopathy
  • p.Gly816= Single submitter Compton-North congenital myopathy
  • p.Gly82= Single submitter Compton-North congenital myopathy
  • p.Gly882= Single submitter Compton-North congenital myopathy
  • p.Gly888= Single submitter Compton-North congenital myopathy
  • p.Gly918= Single submitter Compton-North congenital myopathy
  • p.Gly970= Single submitter Compton-North congenital myopathy
  • p.His336= Single submitter Compton-North congenital myopathy
  • p.His372= Single submitter Compton-North congenital myopathy
  • p.His769= Single submitter Compton-North congenital myopathy
  • p.His960= Single submitter Compton-North congenital myopathy
  • p.Ile434= Single submitter Compton-North congenital myopathy
  • p.Ile516Val Single submitter Compton-North congenital myopathy
  • p.Ile547= Single submitter Compton-North congenital myopathy
  • p.Ile554= Single submitter Compton-North congenital myopathy
  • p.Ile644= Single submitter Compton-North congenital myopathy
  • p.Ile672= Single submitter Compton-North congenital myopathy
  • p.Ile694Thr Single submitter Compton-North congenital myopathy
  • p.Ile923= Single submitter Compton-North congenital myopathy
  • p.Leu19Ser Single submitter Compton-North congenital myopathy
  • p.Leu254= Single submitter Compton-North congenital myopathy
  • p.Leu406= Single submitter Compton-North congenital myopathy
  • p.Leu425= Single submitter Compton-North congenital myopathy
  • p.Leu455= Single submitter Compton-North congenital myopathy
  • p.Leu569= Single submitter
  • p.Leu575= Single submitter Compton-North congenital myopathy
  • p.Leu610= Single submitter Compton-North congenital myopathy
  • p.Leu63= Single submitter Compton-North congenital myopathy
  • p.Leu687= Single submitter Compton-North congenital myopathy
  • p.Leu723= Single submitter Compton-North congenital myopathy
  • p.Leu730= Single submitter Compton-North congenital myopathy
  • p.Leu998Pro Single submitter Inborn genetic diseases ⚠
  • p.Lys105= Single submitter Compton-North congenital myopathy
  • p.Lys220= Single submitter Compton-North congenital myopathy
  • p.Lys277= Single submitter Compton-North congenital myopathy
  • p.Lys636Thr Single submitter Compton-North congenital myopathy
  • p.Lys700= Single submitter
  • p.Lys76= Single submitter Inborn genetic diseases
  • p.Lys818= Single submitter Compton-North congenital myopathy
  • p.Phe1018= Single submitter Compton-North congenital myopathy
  • p.Phe530= Single submitter Compton-North congenital myopathy
  • p.Phe542= Single submitter Compton-North congenital myopathy
  • p.Phe72= Single submitter Compton-North congenital myopathy
  • p.Pro160= Single submitter Compton-North congenital myopathy
  • p.Pro231= Single submitter Compton-North congenital myopathy
  • p.Pro271= Single submitter Compton-North congenital myopathy
  • p.Pro413= Single submitter Compton-North congenital myopathy
  • p.Pro442= Single submitter Compton-North congenital myopathy
  • p.Pro603= Single submitter Compton-North congenital myopathy
  • p.Pro692= Single submitter Compton-North congenital myopathy
  • p.Pro73= Single submitter Compton-North congenital myopathy
  • p.Pro748= Single submitter Compton-North congenital myopathy
  • p.Pro794= Single submitter Compton-North congenital myopathy
  • p.Pro904= Single submitter Compton-North congenital myopathy
  • p.Pro909= Single submitter Compton-North congenital myopathy
  • p.Ser14= Single submitter Compton-North congenital myopathy
  • p.Ser204= Single submitter Compton-North congenital myopathy
  • p.Ser217= Single submitter Compton-North congenital myopathy
  • p.Ser447= Single submitter Compton-North congenital myopathy
  • p.Ser56= Single submitter Compton-North congenital myopathy
  • p.Ser564= Single submitter
  • p.Ser635= Single submitter Compton-North congenital myopathy
  • p.Ser696= Single submitter Compton-North congenital myopathy
  • p.Ser865= Single submitter Compton-North congenital myopathy
  • p.Ser917= Single submitter Compton-North congenital myopathy
  • p.Ser935= Single submitter Compton-North congenital myopathy
  • p.Thr355= Single submitter Compton-North congenital myopathy
  • p.Thr452= Single submitter Compton-North congenital myopathy
  • p.Thr483= Single submitter Compton-North congenital myopathy
  • p.Thr505= Single submitter Compton-North congenital myopathy
  • p.Thr582= Single submitter Compton-North congenital myopathy
  • p.Thr582Ile Single submitter Compton-North congenital myopathy ⚠
  • p.Thr684= Single submitter Compton-North congenital myopathy
  • p.Thr686= Single submitter Compton-North congenital myopathy
  • p.Thr724= Single submitter Compton-North congenital myopathy
  • p.Thr726= Single submitter
  • p.Thr764= Single submitter Compton-North congenital myopathy
  • p.Thr924= Single submitter Compton-North congenital myopathy
  • p.Thr938= Single submitter Compton-North congenital myopathy
  • p.Tyr120= Single submitter Compton-North congenital myopathy
  • p.Tyr240= Single submitter Compton-North congenital myopathy
  • p.Tyr252= Single submitter Compton-North congenital myopathy
  • p.Tyr28= Single submitter Compton-North congenital myopathy
  • p.Tyr75= Single submitter Compton-North congenital myopathy
  • p.Tyr767= Single submitter Compton-North congenital myopathy
  • p.Val146= Single submitter Compton-North congenital myopathy
  • p.Val155= Single submitter Compton-North congenital myopathy
  • p.Val245= Single submitter Compton-North congenital myopathy
  • p.Val259= Single submitter Compton-North congenital myopathy
  • p.Val294= Single submitter Compton-North congenital myopathy
  • p.Val432Met Single submitter Compton-North congenital myopathy ⚠

Uncertain significance 281