Sugi Variant

Sugi Variant/SLC52A2

SLC52A2 — 545 ClinVar variants

All ClinVar germline SLC52A2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 266 flagged for review →

21 Pathogenic · 8 Pathogenic/Likely pathogenic · 12 Likely pathogenic · 23 Conflicting · 6 Benign · 11 Benign/Likely benign · 190 Likely benign · 274 Uncertain significance

Full SLC52A2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 266

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 4

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

Predictors agree, ClinVar conflicts 15

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

Predictors lean, ClinVar uncertain 196

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 196

Predictors split 51

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

All SLC52A2 variants

Pathogenic 21

  • p.Gly306Arg Multiple submitters SLC52A2-related disorder
  • p.Leu339Pro Multiple submitters SLC52A2-related disorder
  • p.Trp198Ter Multiple submitters Brown-Vialetto-van Laere syndrome 2
  • p.Tyr50Ter Multiple submitters Brown-Vialetto-van Laere syndrome 2
  • p.Ala199fs Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Gln251Ter Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Gly182fs Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.His110fs Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Leu123Pro Single submitter mitochondrial disease
  • p.Leu359fs Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Leu365fs Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Leu94fs Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Leu98fs Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Phe19fs Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Pro184fs Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Ser52Phe Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Trp379Ter Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Ala284Asp No assertion criteria Brown-Vialetto-van Laere syndrome 2
  • p.Leu342fs No assertion criteria Auditory neuropathy spectrum disorder
  • p.Phe135del No assertion criteria Brown-Vialetto-van Laere syndrome 2
  • p.Tyr305Cys No assertion criteria Brown-Vialetto-van Laere syndrome 2

Pathogenic/Likely pathogenic 8

  • p.Ala420Thr Multiple submitters SLC52A2-related disorder ⚠
  • p.Gln270Ter Multiple submitters SLC52A2-related disorder
  • p.Leu185fs Multiple submitters Brown-Vialetto-van Laere syndrome 2
  • p.Leu312Pro Multiple submitters SLC52A2-related disorder
  • p.Leu344fs Multiple submitters Brown-Vialetto-van Laere syndrome 2
  • p.Leu381fs Multiple submitters Brown-Vialetto-van Laere syndrome 2
  • p.Pro363Leu Multiple submitters Brown-Vialetto-van Laere syndrome 2
  • p.Ser128Leu Multiple submitters Inborn genetic diseases

Likely pathogenic 12

Conflicting classifications of pathogenicity 23

Benign 6

Benign/Likely benign 11

  • c.1001+6C>T Multiple submitters Brown-Vialetto-van Laere syndrome 2
  • p.Ala103= Multiple submitters Brown-Vialetto-van Laere syndrome 2
  • p.Ala118Asp Multiple submitters Inborn genetic diseases
  • p.Ala296= Multiple submitters Brown-Vialetto-van Laere syndrome 2
  • p.Ala440= Multiple submitters Brown-Vialetto-van Laere syndrome 2
  • p.Gly232= Multiple submitters Brown-Vialetto-van Laere syndrome 2
  • p.Gly415= Multiple submitters Brown-Vialetto-van Laere syndrome 2
  • p.Leu215= Multiple submitters Inborn genetic diseases
  • p.Leu356= Multiple submitters Brown-Vialetto-van Laere syndrome 2
  • p.Pro363= Multiple submitters Brown-Vialetto-van Laere syndrome 2
  • p.Val120Ala Multiple submitters Inborn genetic diseases

Likely benign 190

  • c.1001+20C>T Multiple submitters Brown-Vialetto-van Laere syndrome 2
  • c.131-11C>G Multiple submitters Brown-Vialetto-van Laere syndrome 2
  • c.-106AAG[1] Multiple submitters
  • c.-110-35C>G Multiple submitters
  • p.Ala202= Multiple submitters Inborn genetic diseases
  • p.Ala209= Multiple submitters Inborn genetic diseases
  • p.Ala274= Multiple submitters Brown-Vialetto-van Laere syndrome 2
  • p.Ala284= Multiple submitters Brown-Vialetto-van Laere syndrome 2
  • p.Ala288= Multiple submitters Inborn genetic diseases
  • p.Arg275= Multiple submitters Brown-Vialetto-van Laere syndrome 2
  • p.Arg82= Multiple submitters Brown-Vialetto-van Laere syndrome 2
  • p.Asn28= Multiple submitters Inborn genetic diseases
  • p.Asn287= Multiple submitters Brown-Vialetto-van Laere syndrome 2
  • p.Asp76= Multiple submitters Inborn genetic diseases
  • p.Gly317= Multiple submitters Brown-Vialetto-van Laere syndrome 2
  • p.Gly371= Multiple submitters Inborn genetic diseases
  • p.Gly399= Multiple submitters Brown-Vialetto-van Laere syndrome 2
  • p.Gly409= Multiple submitters Brown-Vialetto-van Laere syndrome 2
  • p.His138= Multiple submitters Brown-Vialetto-van Laere syndrome 2
  • p.His431= Multiple submitters Brown-Vialetto-van Laere syndrome 2
  • p.Leu115= Multiple submitters Brown-Vialetto-van Laere syndrome 2
  • p.Leu121= Multiple submitters Inborn genetic diseases
  • p.Leu139= Multiple submitters Brown-Vialetto-van Laere syndrome 2
  • p.Leu163= Multiple submitters Inborn genetic diseases
  • p.Leu279= Multiple submitters Inborn genetic diseases
  • p.Leu316= Multiple submitters Brown-Vialetto-van Laere syndrome 2
  • p.Leu60= Multiple submitters Brown-Vialetto-van Laere syndrome 2
  • p.Pro176= Multiple submitters Brown-Vialetto-van Laere syndrome 2
  • p.Pro219= Multiple submitters Brown-Vialetto-van Laere syndrome 2
  • p.Pro42= Multiple submitters Brown-Vialetto-van Laere syndrome 2
  • p.Pro48= Multiple submitters Brown-Vialetto-van Laere syndrome 2
  • p.Ser223= Multiple submitters Brown-Vialetto-van Laere syndrome 2
  • p.Ser369= Multiple submitters Brown-Vialetto-van Laere syndrome 2
  • p.Thr12= Multiple submitters Brown-Vialetto-van Laere syndrome 2
  • p.Tyr305= Multiple submitters Inborn genetic diseases
  • p.Val358= Multiple submitters Brown-Vialetto-van Laere syndrome 2
  • c.1001+17A>C Single submitter Brown-Vialetto-van Laere syndrome 2
  • c.1001+17A>T Single submitter
  • c.1001+18G>T Single submitter Brown-Vialetto-van Laere syndrome 2
  • c.1001+45= Single submitter
  • c.1001+9G>A Single submitter Brown-Vialetto-van Laere syndrome 2
  • c.1002-11G>A Single submitter Brown-Vialetto-van Laere syndrome 2
  • c.1002-12C>T Single submitter Brown-Vialetto-van Laere syndrome 2
  • c.1002-15del Single submitter Brown-Vialetto-van Laere syndrome 2
  • c.1002-17C>G Single submitter Brown-Vialetto-van Laere syndrome 2
  • c.1002-17C>T Single submitter Brown-Vialetto-van Laere syndrome 2
  • c.1002-18T>C Single submitter Brown-Vialetto-van Laere syndrome 2
  • c.1002-7A>G Single submitter Brown-Vialetto-van Laere syndrome 2
  • c.1125+14G>T Single submitter Brown-Vialetto-van Laere syndrome 2
  • c.1125+15A>C Single submitter Brown-Vialetto-van Laere syndrome 2
  • c.1125+17A>G Single submitter Brown-Vialetto-van Laere syndrome 2
  • c.1125+7A>G Single submitter
  • c.1125+9_1125+10del Single submitter
  • c.1126-15C>T Single submitter Brown-Vialetto-van Laere syndrome 2
  • c.1126-18G>C Single submitter Brown-Vialetto-van Laere syndrome 2
  • c.1126-5C>T Single submitter Brown-Vialetto-van Laere syndrome 2
  • c.1126-6C>T Single submitter Brown-Vialetto-van Laere syndrome 2
  • c.1126-8C>T Single submitter Brown-Vialetto-van Laere syndrome 2
  • c.1126-9C>T Single submitter Brown-Vialetto-van Laere syndrome 2
  • c.130+11G>A Single submitter
  • c.130+13G>A Single submitter Brown-Vialetto-van Laere syndrome 2
  • c.131-11C>T Single submitter Brown-Vialetto-van Laere syndrome 2
  • c.131-12C>A Single submitter Brown-Vialetto-van Laere syndrome 2
  • c.131-12C>T Single submitter Brown-Vialetto-van Laere syndrome 2
  • c.131-15C>A Single submitter Brown-Vialetto-van Laere syndrome 2
  • c.131-15C>G Single submitter Brown-Vialetto-van Laere syndrome 2
  • c.131-16C>T Single submitter Brown-Vialetto-van Laere syndrome 2
  • c.131-19C>T Single submitter Brown-Vialetto-van Laere syndrome 2
  • c.131-6C>G Single submitter Brown-Vialetto-van Laere syndrome 2
  • c.131-6C>T Single submitter Brown-Vialetto-van Laere syndrome 2
  • c.131-7C>G Single submitter Brown-Vialetto-van Laere syndrome 2
  • c.131-7C>T Single submitter
  • c.131-8C>T Single submitter Brown-Vialetto-van Laere syndrome 2
  • c.-44C>T Single submitter
  • p.Ala106= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Ala113= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Ala155= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Ala175= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Ala193= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Ala199= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Ala237= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Ala319= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Ala355= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Ala370= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Ala404= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Ala407= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Ala408= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Ala411= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Ala72= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Asn178= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Asn59= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Asp441= Single submitter
  • p.Cys159= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Gln151= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Gln234= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Gln251= Single submitter
  • p.Glu189= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Glu228= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Glu246= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Glu252= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Glu77= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Gly152= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Gly168= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Gly182= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Gly227= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Gly230= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Gly29= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Gly292= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Gly306= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Gly330= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Gly341= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Gly346= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Gly351= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Gly384= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Gly400= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Gly419= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Gly58= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.His101= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.His398= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Ile429= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Ile81= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Leu109= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Leu11= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Leu15= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Leu156= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Leu157= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Leu170= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Leu185= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Leu204= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Leu217= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Leu250= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Leu272= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Leu282= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Leu289= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Leu327= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Leu339= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Leu353= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Leu359= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Leu381= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Leu41= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Leu417= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Leu418= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Leu57= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Leu94= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Phe114= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Phe148= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Phe196= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Phe197= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Phe326= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Phe424= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Pro183= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Pro184= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Pro192= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Pro220= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Pro221= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Pro364= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Pro403= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Pro425= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Pro426= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Pro442= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Pro73= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Pro9Leu Single submitter Inborn genetic diseases ⚠
  • p.Ser128= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Ser231= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Ser247= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Ser248= Single submitter
  • p.Ser301= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Ser378= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Ser49= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Ser52Thr Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Thr180= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Thr260= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Thr261= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Thr286= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Thr368= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Thr66= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Tyr388= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Tyr50= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Val167= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Val205= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Val315= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Val331= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Val347= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Val36= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Val37= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Val385= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Val391= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Val53= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Val64= Single submitter Brown-Vialetto-van Laere syndrome 2
  • p.Val366= No assertion criteria SLC52A2-related disorder

Uncertain significance 274