Sugi Variant

Sugi Variant/CDKN2A

CDKN2A — 1310 ClinVar variants

All ClinVar germline CDKN2A variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 474 flagged for review →

69 Pathogenic · 32 Pathogenic/Likely pathogenic · 37 Likely pathogenic · 139 Conflicting · 103 Benign · 59 Benign/Likely benign · 226 Likely benign · 645 Uncertain significance

Full CDKN2A gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 474

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 2

ClinVar calls these pathogenic, but the computational predictors lean tolerated — the highest-value review flag.

Predictors agree, ClinVar conflicts 40

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

Predicted LoF vs a conflicting call 9

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 232

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 232

Predictors split 191

The independent predictors disagree with each other — read with care. · showing the 150 best-reviewed of 191

All CDKN2A variants

Pathogenic 69

  • c.151-1G>A Multiple submitters melanoma-pancreatic cancer syndrome
  • c.151-1G>C Multiple submitters familial melanoma
  • c.194-3653G>T Multiple submitters ovarian neoplasm
  • p.Ala36fs Multiple submitters hereditary neoplastic syndrome
  • p.Arg103fs Multiple submitters familial melanoma
  • p.Arg112dup Multiple submitters familial melanoma
  • p.Arg46fs Multiple submitters familial melanoma
  • p.Arg87Pro Multiple submitters familial melanoma
  • p.Gln50Ter Multiple submitters familial melanoma
  • p.Glu120fs Multiple submitters hereditary neoplastic syndrome
  • p.Glu27Ter Multiple submitters familial melanoma
  • p.Glu88Ter Multiple submitters familial melanoma
  • p.Gly101Trp Multiple submitters melanoma
  • p.His123fs Multiple submitters familial melanoma
  • p.Leu16fs Multiple submitters familial melanoma
  • p.Leu32_Leu37del Multiple submitters familial melanoma
  • p.Leu64fs Multiple submitters hereditary neoplastic syndrome
  • p.Pro41fs Multiple submitters hereditary neoplastic syndrome
  • p.Pro81fs Multiple submitters hereditary neoplastic syndrome
  • p.Ser12Ter Multiple submitters familial melanoma
  • p.Ser43_Tyr44insTer Multiple submitters familial melanoma
  • p.Ser43Ter Multiple submitters hereditary neoplastic syndrome
  • p.Ser8fs Multiple submitters familial melanoma
  • p.Trp110Ter Multiple submitters familial melanoma
  • p.Trp15Ter Multiple submitters hereditary neoplastic syndrome
  • p.Tyr44Ter Multiple submitters hereditary neoplastic syndrome
  • p.Val126Asp Multiple submitters melanoma, cutaneous malignant, susceptibility to, 2
  • c.151-861_252del Single submitter familial melanoma
  • c.206_229delAGCCCAACTGCGCCGACCCCGinsCAG Single submitter hereditary neoplastic syndrome
  • c.457+1G>T Single submitter familial melanoma
  • c.457+2T>G Single submitter familial melanoma
  • c.98_150+1488del Single submitter hereditary neoplastic syndrome
  • p.Ala13fs Single submitter hereditary neoplastic syndrome
  • p.Ala68Ter Single submitter familial melanoma
  • p.Arg22fs Single submitter familial melanoma
  • p.Arg24_Val25insTer Single submitter melanoma-pancreatic cancer syndrome
  • p.Arg24fs Single submitter melanoma-pancreatic cancer syndrome
  • p.Arg58fs Single submitter hereditary neoplastic syndrome
  • p.Arg80fs Single submitter familial melanoma
  • p.Gln57Ter Single submitter melanoma-pancreatic cancer syndrome
  • p.Glu10fs Single submitter familial melanoma
  • p.Glu10Ter Single submitter familial melanoma
  • p.Glu119fs Single submitter familial melanoma
  • p.Glu120Ter Single submitter familial melanoma
  • p.Glu26Ter Single submitter familial melanoma
  • p.Glu33fs Single submitter hereditary neoplastic syndrome
  • p.Glu69Ter Single submitter familial melanoma
  • p.Gly111fs Single submitter familial melanoma
  • p.Gly55= Single submitter melanoma-pancreatic cancer syndrome
  • p.Gly55Asp Single submitter familial melanoma
  • p.His66fs Single submitter familial melanoma
  • p.His83fs Single submitter familial melanoma
  • p.Leu62fs Single submitter hereditary neoplastic syndrome
  • p.Pro48fs Single submitter melanoma-pancreatic cancer syndrome
  • p.Ser12fs Single submitter familial melanoma
  • p.Ser56fs Single submitter familial melanoma
  • p.Ser7fs Single submitter melanoma-pancreatic cancer syndrome
  • p.Thr18fs Single submitter hereditary neoplastic syndrome
  • p.Thr77fs Single submitter hereditary neoplastic syndrome
  • p.Tyr129fs Single submitter familial melanoma
  • p.Tyr129Ter Single submitter familial melanoma
  • p.Tyr44fs Single submitter familial melanoma
  • p.Val115fs Single submitter hereditary neoplastic syndrome
  • p.Val28_Glu33del Single submitter melanoma, cutaneous malignant, susceptibility to, 2
  • p.Val43fs Single submitter familial melanoma
  • p.Val59fs Single submitter hereditary neoplastic syndrome
  • p.Val95fs Single submitter familial melanoma
  • p.Val96fs Single submitter hereditary neoplastic syndrome
  • c.458-521G>T No assertion criteria gastric cancer

Pathogenic/Likely pathogenic 32

  • c.151-1G>T Multiple submitters hereditary neoplastic syndrome
  • c.151-2A>G Multiple submitters familial pancreatic carcinoma
  • c.193+1G>A Multiple submitters familial melanoma
  • c.193+5G>A Multiple submitters familial melanoma
  • c.457+1_457+10del Multiple submitters melanoma and neural system tumor syndrome
  • c.458-105A>G Multiple submitters familial melanoma
  • p.Ala102fs Multiple submitters familial melanoma
  • p.Ala4_Pro11dup Multiple submitters familial melanoma
  • p.Ala76fs Multiple submitters hereditary neoplastic syndrome
  • p.Arg112Gly Multiple submitters familial melanoma
  • p.Arg24Pro Multiple submitters hereditary neoplastic syndrome
  • p.Arg80Ter Multiple submitters hereditary neoplastic syndrome
  • p.Asn71fs Multiple submitters hereditary neoplastic syndrome
  • p.Asp14fs Multiple submitters hereditary neoplastic syndrome
  • p.Asp153Tyr Multiple submitters hereditary neoplastic syndrome ⚠
  • p.Asp84Ala Multiple submitters hereditary neoplastic syndrome
  • p.Gln50Arg Multiple submitters hereditary neoplastic syndrome
  • p.Gly23Arg Multiple submitters familial melanoma
  • p.Gly23Asp Multiple submitters familial melanoma
  • p.Gly65Arg Multiple submitters hereditary neoplastic syndrome
  • p.Gly89Asp Multiple submitters melanoma-pancreatic cancer syndrome
  • p.Ile49Ser Multiple submitters familial melanoma
  • p.Leu121fs Multiple submitters familial melanoma
  • p.Leu16Arg Multiple submitters hereditary neoplastic syndrome
  • p.Leu16Pro Multiple submitters hereditary neoplastic syndrome
  • p.Leu32Pro Multiple submitters familial melanoma
  • p.Leu97fs Multiple submitters familial melanoma
  • p.Pro114fs Multiple submitters hereditary neoplastic syndrome
  • p.Pro48Leu Multiple submitters familial melanoma
  • p.Pro48Thr Multiple submitters familial melanoma
  • p.Ser56Ile Multiple submitters melanoma-pancreatic cancer syndrome
  • p.Val59Gly Multiple submitters melanoma, cutaneous malignant, susceptibility to, 2

Likely pathogenic 37

  • c.150+1G>A Multiple submitters melanoma-pancreatic cancer syndrome
  • c.150+2T>G Multiple submitters hereditary neoplastic syndrome
  • c.193+1del Multiple submitters familial melanoma
  • c.193+2T>C Multiple submitters hereditary neoplastic syndrome
  • p.Ala68Leu Multiple submitters hereditary neoplastic syndrome
  • p.Arg87Trp Multiple submitters melanoma-pancreatic cancer syndrome
  • p.Arg99Pro Multiple submitters hereditary neoplastic syndrome
  • p.Asn71Lys Multiple submitters melanoma-pancreatic cancer syndrome
  • p.Asn71Ser Multiple submitters familial melanoma ⚠
  • p.Asp108Tyr Multiple submitters hereditary neoplastic syndrome
  • p.Asp84Asn Multiple submitters hereditary neoplastic syndrome
  • p.Gln50Pro Multiple submitters hereditary neoplastic syndrome
  • p.Gly23Cys Multiple submitters familial melanoma
  • p.Gly23Ser Multiple submitters hereditary neoplastic syndrome
  • p.Pro81Leu Multiple submitters familial melanoma
  • c.150+1del Single submitter familial melanoma
  • c.150+276T>G Single submitter melanoma-pancreatic cancer syndrome
  • c.150+2T>C Single submitter familial melanoma
  • c.151-16_151-1del Single submitter
  • c.151-6_151delinsC Single submitter acute lymphoblastic leukemia
  • c.194-3712_194-3710del Single submitter melanoma-pancreatic cancer syndrome
  • c.457+1G>A Single submitter hereditary neoplastic syndrome
  • c.99_150+1161del Single submitter melanoma, cutaneous malignant, susceptibility to, 2
  • p.Ala60Glu Single submitter hereditary neoplastic syndrome
  • p.Arg128fs Single submitter familial melanoma
  • p.Arg19Ter Single submitter familial melanoma
  • p.Asp74fs Single submitter melanoma-pancreatic cancer syndrome
  • p.Asp84Val Single submitter familial melanoma
  • p.Asp92fs Single submitter melanoma-pancreatic cancer syndrome
  • p.Leu30fs Single submitter familial melanoma
  • p.Leu63fs Single submitter melanoma and neural system tumor syndrome
  • p.Leu94Pro Single submitter
  • p.Met1Lys Single submitter melanoma-pancreatic cancer syndrome
  • p.Phe90fs Single submitter melanoma-pancreatic cancer syndrome
  • p.Pro114Arg Single submitter hereditary neoplastic syndrome
  • p.Val82fs Single submitter melanoma and neural system tumor syndrome
  • p.Leu78fs No assertion criteria lip and oral cavity carcinoma

Conflicting classifications of pathogenicity 139

Benign 103

  • c.150+1255C>A Multiple submitters melanoma, cutaneous malignant, susceptibility to, 2
  • c.193+174A>G Multiple submitters
  • c.194-3810G>A Multiple submitters squamous cell lung carcinoma
  • c.458-471G>T Multiple submitters
  • c.*29G>C Multiple submitters squamous cell lung carcinoma
  • c.*373C>G Multiple submitters
  • c.*69C>T Multiple submitters
  • p.Ala148Thr Multiple submitters familial pancreatic carcinoma
  • c.150+1255C>T Single submitter melanoma-pancreatic cancer syndrome
  • c.150+214del Single submitter
  • c.150+459T>C Single submitter
  • c.151-782G>C Single submitter
  • c.193+9477T>G Single submitter familial melanoma
  • c.458-101G>A Single submitter melanoma-pancreatic cancer syndrome
  • c.458-103A>T Single submitter melanoma-pancreatic cancer syndrome
  • c.458-107C>G Single submitter melanoma-pancreatic cancer syndrome
  • c.458-108T>A Single submitter melanoma-pancreatic cancer syndrome
  • c.458-108T>C Single submitter melanoma-pancreatic cancer syndrome
  • c.458-110T>A Single submitter melanoma-pancreatic cancer syndrome
  • c.458-21T>C Single submitter melanoma-pancreatic cancer syndrome
  • c.458-22G>A Single submitter melanoma-pancreatic cancer syndrome
  • c.458-23T>C Single submitter melanoma-pancreatic cancer syndrome
  • c.458-24C>A Single submitter melanoma-pancreatic cancer syndrome
  • c.458-25C>T Single submitter melanoma-pancreatic cancer syndrome
  • c.458-26G>A Single submitter melanoma-pancreatic cancer syndrome
  • c.458-26G>C Single submitter melanoma-pancreatic cancer syndrome
  • c.458-26G>T Single submitter melanoma-pancreatic cancer syndrome
  • c.458-27C>T Single submitter melanoma-pancreatic cancer syndrome
  • c.458-29A>T Single submitter melanoma-pancreatic cancer syndrome
  • c.458-30T>A Single submitter melanoma-pancreatic cancer syndrome
  • c.458-35G>T Single submitter melanoma-pancreatic cancer syndrome
  • c.458-36G>A Single submitter melanoma-pancreatic cancer syndrome
  • c.458-38C>T Single submitter melanoma-pancreatic cancer syndrome
  • c.458-39T>C Single submitter melanoma-pancreatic cancer syndrome
  • c.458-39T>G Single submitter melanoma-pancreatic cancer syndrome
  • c.458-40C>T Single submitter melanoma-pancreatic cancer syndrome
  • c.458-44T>G Single submitter melanoma-pancreatic cancer syndrome
  • c.458-46T>A Single submitter melanoma-pancreatic cancer syndrome
  • c.458-46T>C Single submitter melanoma-pancreatic cancer syndrome
  • c.458-50C>G Single submitter melanoma-pancreatic cancer syndrome
  • c.458-50C>T Single submitter melanoma-pancreatic cancer syndrome
  • c.458-57T>A Single submitter melanoma-pancreatic cancer syndrome
  • c.458-57T>G Single submitter melanoma-pancreatic cancer syndrome
  • c.458-58G>A Single submitter melanoma-pancreatic cancer syndrome
  • c.458-60A>C Single submitter melanoma-pancreatic cancer syndrome
  • c.458-60A>G Single submitter melanoma-pancreatic cancer syndrome
  • c.458-60A>T Single submitter melanoma-pancreatic cancer syndrome
  • c.458-60dup Single submitter melanoma-pancreatic cancer syndrome
  • c.458-61G>A Single submitter melanoma-pancreatic cancer syndrome
  • c.458-62G>A Single submitter melanoma-pancreatic cancer syndrome
  • c.458-63G>A Single submitter melanoma-pancreatic cancer syndrome
  • c.458-64C>A Single submitter melanoma-pancreatic cancer syndrome
  • c.458-64C>G Single submitter melanoma-pancreatic cancer syndrome
  • c.458-64C>T Single submitter melanoma-pancreatic cancer syndrome
  • c.458-64del Single submitter melanoma-pancreatic cancer syndrome
  • c.458-65G>A Single submitter melanoma-pancreatic cancer syndrome
  • c.458-66G>A Single submitter melanoma-pancreatic cancer syndrome
  • c.458-67G>A Single submitter melanoma-pancreatic cancer syndrome
  • c.458-67G>C Single submitter melanoma-pancreatic cancer syndrome
  • c.458-68A>G Single submitter melanoma-pancreatic cancer syndrome
  • c.458-69G>A Single submitter melanoma-pancreatic cancer syndrome
  • c.458-71A>T Single submitter melanoma-pancreatic cancer syndrome
  • c.458-75_458-68dup Single submitter melanoma-pancreatic cancer syndrome
  • c.458-79G>A Single submitter melanoma-pancreatic cancer syndrome
  • c.458-80C>T Single submitter melanoma-pancreatic cancer syndrome
  • c.458-82G>A Single submitter melanoma-pancreatic cancer syndrome
  • c.458-83G>A Single submitter melanoma-pancreatic cancer syndrome
  • c.458-85A>C Single submitter melanoma-pancreatic cancer syndrome
  • c.458-87G>A Single submitter melanoma-pancreatic cancer syndrome
  • c.458-88G>A Single submitter melanoma-pancreatic cancer syndrome
  • c.458-88G>T Single submitter melanoma-pancreatic cancer syndrome
  • c.458-89C>T Single submitter melanoma-pancreatic cancer syndrome
  • c.458-90C>A Single submitter melanoma-pancreatic cancer syndrome
  • c.458-90C>G Single submitter melanoma-pancreatic cancer syndrome
  • c.458-90C>T Single submitter melanoma-pancreatic cancer syndrome
  • c.458-92T>A Single submitter melanoma-pancreatic cancer syndrome
  • c.458-92T>C Single submitter melanoma-pancreatic cancer syndrome
  • c.458-93A>G Single submitter melanoma-pancreatic cancer syndrome
  • c.458-93A>T Single submitter melanoma-pancreatic cancer syndrome
  • c.458-94A>G Single submitter melanoma-pancreatic cancer syndrome
  • c.458-99_458-96del Single submitter melanoma-pancreatic cancer syndrome
  • c.*1A>T Single submitter melanoma-pancreatic cancer syndrome
  • c.*223G>T Single submitter
  • c.*4A>G Single submitter melanoma-pancreatic cancer syndrome
  • c.*6C>A Single submitter melanoma-pancreatic cancer syndrome
  • c.*6C>T Single submitter melanoma-pancreatic cancer syndrome
  • c.*7C>T Single submitter melanoma-pancreatic cancer syndrome
  • p.Arg21= Single submitter melanoma-pancreatic cancer syndrome
  • p.Cys15= Single submitter melanoma-pancreatic cancer syndrome
  • p.Gln53= Single submitter melanoma-pancreatic cancer syndrome
  • p.Glu33= Single submitter melanoma-pancreatic cancer syndrome
  • p.Ile11= Single submitter melanoma-pancreatic cancer syndrome
  • p.Leu16= Single submitter melanoma-pancreatic cancer syndrome
  • p.Leu47= Single submitter melanoma-pancreatic cancer syndrome
  • p.Leu60= Single submitter melanoma-pancreatic cancer syndrome
  • p.Leu9= Single submitter melanoma-pancreatic cancer syndrome
  • p.Pro61= Single submitter melanoma-pancreatic cancer syndrome
  • p.Ser7= Single submitter melanoma-pancreatic cancer syndrome
  • p.Thr8= Single submitter melanoma-pancreatic cancer syndrome
  • p.Val2= Single submitter melanoma-pancreatic cancer syndrome
  • p.Val22= Single submitter melanoma-pancreatic cancer syndrome
  • p.Val43= Single submitter melanoma-pancreatic cancer syndrome
  • p.Val7= Single submitter melanoma-pancreatic cancer syndrome

Benign/Likely benign 59

  • c.150+20C>T Multiple submitters familial melanoma
  • c.150+216A>G Multiple submitters melanoma-pancreatic cancer syndrome
  • c.150+7AG[4] Multiple submitters familial melanoma
  • c.151-1238G>A Multiple submitters
  • c.151-14G>A Multiple submitters hereditary neoplastic syndrome
  • c.194-3652G>C Multiple submitters familial melanoma
  • c.458-56G>T Multiple submitters melanoma-pancreatic cancer syndrome
  • c.-25C>T Multiple submitters Li-Fraumeni syndrome
  • c.*6C>G Multiple submitters melanoma-pancreatic cancer syndrome
  • c.*7C>A Multiple submitters melanoma-pancreatic cancer syndrome
  • c.*8A>G Multiple submitters melanoma-pancreatic cancer syndrome
  • c.*9G>A Multiple submitters hereditary neoplastic syndrome
  • p.Ala127Ser Multiple submitters familial melanoma ⚠
  • p.Ala14= Multiple submitters familial melanoma
  • p.Ala17= Multiple submitters hereditary neoplastic syndrome
  • p.Ala19= Multiple submitters hereditary neoplastic syndrome
  • p.Ala34= Multiple submitters familial melanoma
  • p.Ala36= Multiple submitters hereditary neoplastic syndrome
  • p.Ala39= Multiple submitters hereditary neoplastic syndrome
  • p.Ala40= Multiple submitters melanoma-pancreatic cancer syndrome
  • p.Ala42= Multiple submitters familial melanoma
  • p.Ala5= Multiple submitters familial melanoma
  • p.Arg10= Multiple submitters familial melanoma
  • p.Arg128= Multiple submitters hereditary neoplastic syndrome
  • p.Arg13= Multiple submitters hereditary neoplastic syndrome
  • p.Arg24= Multiple submitters hereditary neoplastic syndrome
  • p.Arg29= Multiple submitters melanoma-pancreatic cancer syndrome
  • p.Arg3= Multiple submitters melanoma-pancreatic cancer syndrome
  • p.Arg51= Multiple submitters familial melanoma
  • p.Arg58= Multiple submitters Li-Fraumeni syndrome
  • p.Asn42= Multiple submitters hereditary neoplastic syndrome
  • p.Asp156= Multiple submitters familial melanoma
  • p.Glu26= Multiple submitters familial melanoma
  • p.Gly32= Multiple submitters melanoma-pancreatic cancer syndrome
  • p.Gly56= Multiple submitters familial melanoma
  • p.His26= Multiple submitters familial melanoma
  • p.Ile154= Multiple submitters familial melanoma
  • p.Ile49= Multiple submitters familial melanoma
  • p.Leu30= Multiple submitters familial melanoma
  • p.Leu32= Multiple submitters familial melanoma
  • p.Leu45= Multiple submitters familial melanoma
  • p.Leu49= Multiple submitters hereditary neoplastic syndrome
  • p.Leu55= Multiple submitters hereditary neoplastic syndrome
  • p.Phe23= Multiple submitters hereditary neoplastic syndrome
  • p.Phe5= Multiple submitters familial melanoma
  • p.Pro17= Multiple submitters familial melanoma
  • p.Pro18= Multiple submitters familial melanoma
  • p.Pro28= Multiple submitters familial melanoma
  • p.Pro3= Multiple submitters familial melanoma
  • p.Pro37= Multiple submitters familial melanoma
  • p.Pro38= Multiple submitters familial melanoma
  • p.Pro41= Multiple submitters melanoma-pancreatic cancer syndrome
  • p.Ser12= Multiple submitters melanoma-pancreatic cancer syndrome
  • p.Ser43= Multiple submitters hereditary neoplastic syndrome
  • p.Thr31= Multiple submitters familial melanoma
  • p.Tyr44= Multiple submitters melanoma-pancreatic cancer syndrome
  • p.Val24= Multiple submitters familial melanoma
  • p.Val25= Multiple submitters hereditary neoplastic syndrome
  • p.Val46= Multiple submitters familial melanoma

Likely benign 226

Uncertain significance 645

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