Sugi Variant

Sugi Variant/AMPD2

AMPD2 — 532 ClinVar variants

All ClinVar germline AMPD2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 156 flagged for review →

22 Pathogenic · 7 Pathogenic/Likely pathogenic · 19 Likely pathogenic · 10 Conflicting · 38 Benign · 9 Benign/Likely benign · 211 Likely benign · 216 Uncertain significance

Full AMPD2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 156

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 7

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

Predictors lean, ClinVar uncertain 118

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

Predictors split 31

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

All AMPD2 variants

Pathogenic 22

  • c.531+2T>G Single submitter
  • c.532-1G>T Single submitter congenital nervous system disorder
  • c.-42dup Single submitter pontocerebellar hypoplasia type 9
  • c.-43_-24dup Single submitter hereditary spastic paraplegia 63
  • c.-90_-69dup Single submitter pontocerebellar hypoplasia type 9
  • p.Ala89fs Single submitter hereditary spastic paraplegia 63
  • p.Arg270fs Single submitter spastic ataxia
  • p.Arg45fs Single submitter
  • p.Gln107Ter Single submitter hereditary spastic paraplegia 63
  • p.Gln400Ter Single submitter pontocerebellar hypoplasia type 9
  • p.Glu724Asp Single submitter pontocerebellar hypoplasia
  • p.Glu83Ter Single submitter pontocerebellar hypoplasia type 9
  • p.Leu722Arg Single submitter pontocerebellar hypoplasia type 9
  • p.Lys14fs Single submitter pontocerebellar hypoplasia type 9
  • p.Tyr295_Pro296insTer Single submitter hereditary spastic paraplegia 63
  • p.Tyr669Ter Single submitter pontocerebellar hypoplasia type 9
  • p.Asp739Tyr No assertion criteria pontocerebellar hypoplasia type 9
  • p.Cys53fs No assertion criteria hereditary spastic paraplegia 63
  • p.Gln112fs No assertion criteria pontocerebellar hypoplasia type 9
  • p.Gln299Ter No assertion criteria pontocerebellar hypoplasia type 9
  • p.Tyr295Ter No assertion criteria pontocerebellar hypoplasia type 9
  • p.Tyr698Ter No assertion criteria pontocerebellar hypoplasia type 9

Pathogenic/Likely pathogenic 7

  • c.1698+1G>A Multiple submitters hereditary spastic paraplegia 63
  • p.Arg353Ter Multiple submitters pontocerebellar hypoplasia type 9
  • p.Arg449Ter Multiple submitters pontocerebellar hypoplasia
  • p.Arg620His Multiple submitters pontocerebellar hypoplasia type 9
  • p.Glu174Ter Multiple submitters pontocerebellar hypoplasia type 9
  • p.Gly35fs Multiple submitters hereditary spastic paraplegia 63
  • p.Leu216fs Multiple submitters hereditary spastic paraplegia 63

Likely pathogenic 19

  • p.Arg789His Multiple submitters pontocerebellar hypoplasia
  • p.Glu85fs Multiple submitters pontocerebellar hypoplasia type 9
  • c.1080+2T>G Single submitter pontocerebellar hypoplasia type 9
  • c.1408-3_1418del Single submitter pontocerebellar hypoplasia type 9
  • c.1983+1G>A Single submitter pontocerebellar hypoplasia type 9
  • c.1984-2A>G Single submitter hereditary spastic paraplegia 63
  • c.861-2A>G Single submitter hereditary spastic paraplegia 63
  • c.91+1G>T Single submitter hereditary spastic paraplegia 63
  • p.Ala729Pro Single submitter pontocerebellar hypoplasia type 9
  • p.Arg324Pro Single submitter Inborn genetic diseases
  • p.Arg620Leu Single submitter pontocerebellar hypoplasia type 9
  • p.Arg620Ser Single submitter pontocerebellar hypoplasia type 9
  • p.Asn357Ser Single submitter Inborn genetic diseases
  • p.Gln101fs Single submitter hereditary spastic paraplegia 63
  • p.Gly491Arg Single submitter hereditary spastic paraplegia 63
  • p.Pro442fs Single submitter pontocerebellar hypoplasia type 9
  • p.Pro90fs Single submitter hereditary spastic paraplegia 63
  • p.Trp594Ter Single submitter hereditary spastic paraplegia 63
  • p.Tyr91fs Single submitter

Conflicting classifications of pathogenicity 10

Benign 38

Benign/Likely benign 9

  • c.1080+9T>C Multiple submitters hereditary spastic paraplegia 63
  • c.1276-20A>G Multiple submitters hereditary spastic paraplegia 63
  • c.1408-12C>T Multiple submitters pontocerebellar hypoplasia type 9
  • c.223-4C>T Multiple submitters hereditary spastic paraplegia 63
  • c.-52C>G Multiple submitters pontocerebellar hypoplasia type 9
  • p.Gln825= Multiple submitters hereditary spastic paraplegia 63
  • p.Ser572= Multiple submitters pontocerebellar hypoplasia type 9
  • p.Thr401= Multiple submitters pontocerebellar hypoplasia type 9
  • p.Thr529= Multiple submitters hereditary spastic paraplegia 63

Likely benign 211

  • c.1571+124A>G Multiple submitters
  • c.1699-11T>C Multiple submitters pontocerebellar hypoplasia type 9
  • c.1699-12G>T Multiple submitters pontocerebellar hypoplasia type 9
  • c.1983+47T>C Multiple submitters
  • c.1983+54C>A Multiple submitters
  • c.531+149C>T Multiple submitters
  • c.91+170T>G Multiple submitters
  • c.-263+95A>G Multiple submitters
  • p.Ala32= Multiple submitters hereditary spastic paraplegia 63
  • p.Ala73= Multiple submitters pontocerebellar hypoplasia type 9
  • p.Ile391= Multiple submitters hereditary spastic paraplegia 63
  • p.Leu194= Multiple submitters pontocerebellar hypoplasia type 9
  • p.Lys578= Multiple submitters pontocerebellar hypoplasia type 9
  • p.Pro179= Multiple submitters pontocerebellar hypoplasia type 9
  • p.Pro233= Multiple submitters pontocerebellar hypoplasia type 9
  • p.Pro242= Multiple submitters hereditary spastic paraplegia 63
  • p.Pro442= Multiple submitters pontocerebellar hypoplasia type 9
  • p.Ser708= Multiple submitters pontocerebellar hypoplasia type 9
  • p.Val664= Multiple submitters pontocerebellar hypoplasia type 9
  • c.1080+15C>T Single submitter pontocerebellar hypoplasia type 9
  • c.1080+16G>A Single submitter hereditary spastic paraplegia 63
  • c.1080+18G>A Single submitter hereditary spastic paraplegia 63
  • c.1080+8C>T Single submitter pontocerebellar hypoplasia type 9
  • c.1081-16C>T Single submitter hereditary spastic paraplegia 63
  • c.1081-18T>C Single submitter pontocerebellar hypoplasia type 9
  • c.1275+15C>T Single submitter hereditary spastic paraplegia 63
  • c.1276-11A>G Single submitter hereditary spastic paraplegia 63
  • c.1276-13C>T Single submitter hereditary spastic paraplegia 63
  • c.1276-18C>G Single submitter hereditary spastic paraplegia 63
  • c.1276-4C>T Single submitter hereditary spastic paraplegia 63
  • c.1571+19G>A Single submitter hereditary spastic paraplegia 63
  • c.1571+9C>T Single submitter pontocerebellar hypoplasia type 9
  • c.1572-13G>T Single submitter hereditary spastic paraplegia 63
  • c.1698+13C>T Single submitter hereditary spastic paraplegia 63
  • c.1699-5A>G Single submitter pontocerebellar hypoplasia type 9
  • c.1699-9C>A Single submitter hereditary spastic paraplegia 63
  • c.1862+10C>G Single submitter hereditary spastic paraplegia 63
  • c.1862+10C>T Single submitter pontocerebellar hypoplasia type 9
  • c.1862+16T>C Single submitter pontocerebellar hypoplasia type 9
  • c.1863-6C>T Single submitter hereditary spastic paraplegia 63
  • c.1863-7C>G Single submitter pontocerebellar hypoplasia type 9
  • c.1863-7C>T Single submitter hereditary spastic paraplegia 63
  • c.189C>A Single submitter
  • c.1983+15C>T Single submitter hereditary spastic paraplegia 63
  • c.2157+14_2157+15delinsCC Single submitter hereditary spastic paraplegia 63
  • c.2157+16G>T Single submitter pontocerebellar hypoplasia type 9
  • c.2157+67G>A Single submitter
  • c.2157+77G>T Single submitter
  • c.2158-14C>T Single submitter hereditary spastic paraplegia 63
  • c.2158-17G>A Single submitter pontocerebellar hypoplasia type 9
  • c.2158-18G>T Single submitter hereditary spastic paraplegia 63
  • c.2158-19G>A Single submitter hereditary spastic paraplegia 63
  • c.2158-6G>C Single submitter hereditary spastic paraplegia 63
  • c.222+15C>T Single submitter hereditary spastic paraplegia 63
  • c.222+19C>T Single submitter pontocerebellar hypoplasia type 9
  • c.222+20G>T Single submitter hereditary spastic paraplegia 63
  • c.2268+10C>T Single submitter pontocerebellar hypoplasia type 9
  • c.2268+11G>A Single submitter hereditary spastic paraplegia 63
  • c.2268+11G>C Single submitter hereditary spastic paraplegia 63
  • c.2268+18T>C Single submitter hereditary spastic paraplegia 63
  • c.2269-11G>A Single submitter hereditary spastic paraplegia 63
  • c.2269-12C>T Single submitter hereditary spastic paraplegia 63
  • c.2269-13C>T Single submitter hereditary spastic paraplegia 63
  • c.2269-9T>G Single submitter pontocerebellar hypoplasia type 9
  • c.353+10G>A Single submitter pontocerebellar hypoplasia type 9
  • c.353+8C>A Single submitter hereditary spastic paraplegia 63
  • c.353+8C>T Single submitter pontocerebellar hypoplasia type 9
  • c.353+9G>A Single submitter pontocerebellar hypoplasia type 9
  • c.354-16C>T Single submitter hereditary spastic paraplegia 63
  • c.354-20C>T Single submitter hereditary spastic paraplegia 63
  • c.354-43G>A Single submitter
  • c.423-10C>T Single submitter hereditary spastic paraplegia 63
  • c.423-20C>T Single submitter hereditary spastic paraplegia 63
  • c.423-6C>G Single submitter hereditary spastic paraplegia 63
  • c.531+12G>A Single submitter pontocerebellar hypoplasia type 9
  • c.531+29C>T Single submitter
  • c.532-11C>G Single submitter pontocerebellar hypoplasia type 9
  • c.532-19C>T Single submitter hereditary spastic paraplegia 63
  • c.718+11C>G Single submitter hereditary spastic paraplegia 63
  • c.719-13C>T Single submitter hereditary spastic paraplegia 63
  • c.719-8C>T Single submitter hereditary spastic paraplegia 63
  • c.861-11C>T Single submitter pontocerebellar hypoplasia type 9
  • c.91+139G>A Single submitter
  • c.91+158T>G Single submitter
  • c.91+165A>G Single submitter
  • c.91+78C>A Single submitter
  • c.91+9G>A Single submitter pontocerebellar hypoplasia type 9
  • c.92-15T>C Single submitter hereditary spastic paraplegia 63
  • c.92-200G>A Single submitter
  • c.950+12G>C Single submitter hereditary spastic paraplegia 63
  • c.950+19C>A Single submitter hereditary spastic paraplegia 63
  • c.951-7T>C Single submitter hereditary spastic paraplegia 63
  • c.951-8A>T Single submitter pontocerebellar hypoplasia type 9
  • c.-112G>A Single submitter pontocerebellar hypoplasia type 9
  • c.-132C>T Single submitter hereditary spastic paraplegia 63
  • c.-133C>T Single submitter hereditary spastic paraplegia 63
  • c.-13C>T Single submitter pontocerebellar hypoplasia type 9
  • c.-142C>T Single submitter hereditary spastic paraplegia 63
  • c.-151T>C Single submitter hereditary spastic paraplegia 63
  • c.-19C>T Single submitter pontocerebellar hypoplasia type 9
  • c.-43G>T Single submitter pontocerebellar hypoplasia type 9
  • c.-67T>C Single submitter hereditary spastic paraplegia 63
  • c.-94G>T Single submitter hereditary spastic paraplegia 63
  • c.-97G>A Single submitter pontocerebellar hypoplasia type 9
  • c.-97G>T Single submitter pontocerebellar hypoplasia type 9
  • c.*4T>C Single submitter
  • p.Ala193= Single submitter hereditary spastic paraplegia 63
  • p.Ala247= Single submitter hereditary spastic paraplegia 63
  • p.Ala345= Single submitter hereditary spastic paraplegia 63
  • p.Ala38= Single submitter
  • p.Ala413= Single submitter hereditary spastic paraplegia 63
  • p.Ala501= Single submitter hereditary spastic paraplegia 63
  • p.Ala504= Single submitter pontocerebellar hypoplasia type 9
  • p.Ala593= Single submitter hereditary spastic paraplegia 63
  • p.Ala816= Single submitter pontocerebellar hypoplasia type 9
  • p.Arg106= Single submitter pontocerebellar hypoplasia type 9
  • p.Arg156= Single submitter hereditary spastic paraplegia 63
  • p.Arg158= Single submitter pontocerebellar hypoplasia type 9
  • p.Arg192= Single submitter hereditary spastic paraplegia 63
  • p.Arg382= Single submitter hereditary spastic paraplegia 63
  • p.Arg386= Single submitter hereditary spastic paraplegia 63
  • p.Arg45= Single submitter hereditary spastic paraplegia 63
  • p.Arg508= Single submitter pontocerebellar hypoplasia type 9
  • p.Arg745= Single submitter pontocerebellar hypoplasia type 9
  • p.Arg79= Single submitter pontocerebellar hypoplasia type 9
  • p.Asn581= Single submitter pontocerebellar hypoplasia type 9
  • p.Asp152= Single submitter hereditary spastic paraplegia 63
  • p.Asp474= Single submitter hereditary spastic paraplegia 63
  • p.Asp568= Single submitter hereditary spastic paraplegia 63
  • p.Asp575= Single submitter pontocerebellar hypoplasia type 9
  • p.Asp60= Single submitter hereditary spastic paraplegia 63
  • p.Cys370= Single submitter hereditary spastic paraplegia 63
  • p.Gln107= Single submitter hereditary spastic paraplegia 63
  • p.Gln129= Single submitter hereditary spastic paraplegia 63
  • p.Gln333= Single submitter pontocerebellar hypoplasia type 9
  • p.Gln537= Single submitter hereditary spastic paraplegia 63
  • p.Glu110= Single submitter hereditary spastic paraplegia 63
  • p.Glu292= Single submitter pontocerebellar hypoplasia type 9
  • p.Glu399= Single submitter hereditary spastic paraplegia 63
  • p.Glu587= Single submitter hereditary spastic paraplegia 63
  • p.Glu592= Single submitter
  • p.Glu71= Single submitter pontocerebellar hypoplasia type 9
  • p.Glu92= Single submitter hereditary spastic paraplegia 63
  • p.Gly263= Single submitter hereditary spastic paraplegia 63
  • p.Gly461= Single submitter hereditary spastic paraplegia 63
  • p.Gly7= Single submitter pontocerebellar hypoplasia type 9
  • p.Gly9= Single submitter pontocerebellar hypoplasia type 9
  • p.His277= Single submitter hereditary spastic paraplegia 63
  • p.His393= Single submitter hereditary spastic paraplegia 63
  • p.His566= Single submitter Inborn genetic diseases
  • p.Ile443= Single submitter hereditary spastic paraplegia 63
  • p.Ile468= Single submitter hereditary spastic paraplegia 63
  • p.Ile674= Single submitter hereditary spastic paraplegia 63
  • p.Ile72= Single submitter pontocerebellar hypoplasia type 9
  • p.Ile728= Single submitter hereditary spastic paraplegia 63
  • p.Ile99= Single submitter
  • p.Leu337= Single submitter pontocerebellar hypoplasia type 9
  • p.Leu416= Single submitter pontocerebellar hypoplasia type 9
  • p.Leu59= Single submitter pontocerebellar hypoplasia type 9
  • p.Leu606= Single submitter pontocerebellar hypoplasia type 9
  • p.Leu657= Single submitter hereditary spastic paraplegia 63
  • p.Leu668= Single submitter pontocerebellar hypoplasia type 9
  • p.Leu671= Single submitter hereditary spastic paraplegia 63
  • p.Leu688= Single submitter pontocerebellar hypoplasia type 9
  • p.Phe165= Single submitter pontocerebellar hypoplasia type 9
  • p.Phe548= Single submitter pontocerebellar hypoplasia type 9
  • p.Phe717= Single submitter hereditary spastic paraplegia 63
  • p.Phe93= Single submitter hereditary spastic paraplegia 63
  • p.Pro236= Single submitter hereditary spastic paraplegia 63
  • p.Pro245= Single submitter
  • p.Pro252= Single submitter pontocerebellar hypoplasia type 9
  • p.Pro316= Single submitter hereditary spastic paraplegia 63
  • p.Pro40= Single submitter hereditary spastic paraplegia 63
  • p.Pro48= Single submitter hereditary spastic paraplegia 63
  • p.Pro50= Single submitter hereditary spastic paraplegia 63
  • p.Pro58= Single submitter hereditary spastic paraplegia 63
  • p.Pro663= Single submitter pontocerebellar hypoplasia type 9
  • p.Pro764= Single submitter hereditary spastic paraplegia 63
  • p.Pro90= Single submitter hereditary spastic paraplegia 63
  • p.Pro94= Single submitter hereditary spastic paraplegia 63
  • p.Pro98= Single submitter hereditary spastic paraplegia 63
  • p.Ser22= Single submitter hereditary spastic paraplegia 63
  • p.Ser446= Single submitter hereditary spastic paraplegia 63
  • p.Ser493= Single submitter hereditary spastic paraplegia 63
  • p.Ser577= Single submitter
  • p.Ser645= Single submitter pontocerebellar hypoplasia type 9
  • p.Ser747= Single submitter pontocerebellar hypoplasia type 9
  • p.Ser751= Single submitter pontocerebellar hypoplasia type 9
  • p.Ser84= Single submitter pontocerebellar hypoplasia type 9
  • p.Thr134= Single submitter hereditary spastic paraplegia 63
  • p.Thr211= Single submitter pontocerebellar hypoplasia type 9
  • p.Thr235= Single submitter hereditary spastic paraplegia 63
  • p.Thr27= Single submitter hereditary spastic paraplegia 63
  • p.Thr455= Single submitter hereditary spastic paraplegia 63
  • p.Thr627= Single submitter pontocerebellar hypoplasia type 9
  • p.Thr63= Single submitter pontocerebellar hypoplasia type 9
  • p.Thr709= Single submitter pontocerebellar hypoplasia type 9
  • p.Thr718= Single submitter pontocerebellar hypoplasia type 9
  • p.Thr801= Single submitter pontocerebellar hypoplasia type 9
  • p.Tyr279= Single submitter pontocerebellar hypoplasia type 9
  • p.Tyr327= Single submitter hereditary spastic paraplegia 63
  • p.Tyr490= Single submitter hereditary spastic paraplegia 63
  • p.Tyr726= Single submitter hereditary spastic paraplegia 63
  • p.Tyr790= Single submitter pontocerebellar hypoplasia type 9
  • p.Val350= Single submitter pontocerebellar hypoplasia type 9
  • p.Val583= Single submitter hereditary spastic paraplegia 63
  • p.Val732= Single submitter hereditary spastic paraplegia 63
  • p.Cys288= No assertion criteria AMPD2-related disorder
  • p.Gln146Arg No assertion criteria intellectual disability
  • p.Glu343= No assertion criteria AMPD2-related disorder
  • p.Leu421= No assertion criteria AMPD2-related disorder

Uncertain significance 216