Sugi Variant

Sugi Variant/SLC52A3

SLC52A3 — 476 ClinVar variants

All ClinVar germline SLC52A3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 221 flagged for review →

19 Pathogenic · 2 Pathogenic/Likely pathogenic · 12 Likely pathogenic · 20 Conflicting · 27 Benign · 9 Benign/Likely benign · 167 Likely benign · 220 Uncertain significance

Full SLC52A3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 221

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 1

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 169

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 169

Predictors split 36

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

All SLC52A3 variants

Pathogenic 19

  • p.Gln259Ter Multiple submitters Inborn genetic diseases
  • p.Glu184Ter Multiple submitters Brown-Vialetto-van Laere syndrome 1
  • p.Tyr213Ter Multiple submitters SLC52A3-related disorder
  • p.Ala107fs Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Gln285Ter Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Glu249Ter Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Gly162fs Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Leu29fs Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Ser264fs Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Trp17Ter Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Trp24Ter Single submitter progressive bulbar palsy of childhood
  • p.Trp98Ter Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Tyr136Ter Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Tyr287fs Single submitter Likely inborn error of metabolism
  • c.1198-2A>C No assertion criteria progressive bulbar palsy of childhood
  • p.Glu71Ter No assertion criteria Brown-Vialetto-van Laere syndrome 1
  • p.Phe224Leu No assertion criteria Brown-Vialetto-van Laere syndrome 1 ⚠
  • p.Pro28Thr No assertion criteria Brown-Vialetto-van Laere syndrome 1
  • p.Trp17Arg No assertion criteria Brown-Vialetto-van Laere syndrome 1

Pathogenic/Likely pathogenic 2

  • p.Ala312Val Multiple submitters Brown-Vialetto-van Laere syndrome 1 ⚠
  • p.Val252fs Multiple submitters Inborn genetic diseases

Likely pathogenic 12

  • p.Leu442fs Multiple submitters Brown-Vialetto-van Laere syndrome 1
  • p.Asn94fs Single submitter SLC52A3-related disorder
  • p.Gly439Asp Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Leu221fs Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Leu235Pro Single submitter auditory neuropathy
  • p.Leu438Pro Single submitter Inborn genetic diseases
  • p.Leu445Arg Single submitter
  • p.Ser219Ter Single submitter SLC52A3-related disorder
  • p.Ser402fs Single submitter Inborn genetic diseases
  • p.Thr125Ile Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Trp248fs Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Trp431Ter Single submitter

Conflicting classifications of pathogenicity 20

Benign 27

Benign/Likely benign 9

  • p.Ala312= Multiple submitters Inborn genetic diseases
  • p.Asn21= Multiple submitters Brown-Vialetto-van Laere syndrome 1
  • p.Asp174Gly Multiple submitters Brown-Vialetto-van Laere syndrome 1
  • p.Ile74Met Multiple submitters Brown-Vialetto-van Laere syndrome 1
  • p.Leu327= Multiple submitters Inborn genetic diseases
  • p.Leu350Met Multiple submitters Brown-Vialetto-van Laere syndrome 1
  • p.Phe113= Multiple submitters Brown-Vialetto-van Laere syndrome 1
  • p.Phe3= Multiple submitters Inborn genetic diseases
  • p.Thr121= Multiple submitters Inborn genetic diseases

Likely benign 167

  • c.1073+10C>T Multiple submitters Brown-Vialetto-van Laere syndrome 1
  • c.1197+93C>T Multiple submitters
  • c.567+15C>A Multiple submitters Brown-Vialetto-van Laere syndrome 1
  • c.567+16C>T Multiple submitters Brown-Vialetto-van Laere syndrome 1
  • c.568-17T>C Multiple submitters Brown-Vialetto-van Laere syndrome 1
  • p.Ala237= Multiple submitters Brown-Vialetto-van Laere syndrome 1
  • p.Ala298= Multiple submitters Brown-Vialetto-van Laere syndrome 1
  • p.Ala381= Multiple submitters Brown-Vialetto-van Laere syndrome 1
  • p.Arg268= Multiple submitters Brown-Vialetto-van Laere syndrome 1
  • p.Arg426= Multiple submitters Inborn genetic diseases
  • p.Asn311= Multiple submitters Brown-Vialetto-van Laere syndrome 1
  • p.Asn315= Multiple submitters Brown-Vialetto-van Laere syndrome 1
  • p.Glu33Gln Multiple submitters Inborn genetic diseases
  • p.Gly146= Multiple submitters Inborn genetic diseases
  • p.Leu206= Multiple submitters Inborn genetic diseases
  • p.Phe309= Multiple submitters Brown-Vialetto-van Laere syndrome 1
  • p.Pro205= Multiple submitters Brown-Vialetto-van Laere syndrome 1
  • p.Pro267= Multiple submitters Brown-Vialetto-van Laere syndrome 1
  • p.Ser175= Multiple submitters Brown-Vialetto-van Laere syndrome 1
  • p.Ser70= Multiple submitters Inborn genetic diseases
  • p.Thr278= Multiple submitters Brown-Vialetto-van Laere syndrome 1
  • p.Thr45= Multiple submitters Brown-Vialetto-van Laere syndrome 1
  • p.Thr83= Multiple submitters Brown-Vialetto-van Laere syndrome 1
  • p.Tyr329= Multiple submitters Brown-Vialetto-van Laere syndrome 1
  • p.Val365= Multiple submitters Inborn genetic diseases
  • p.Val81Met Multiple submitters Brown-Vialetto-van Laere syndrome 1
  • c.1073+11A>C Single submitter Brown-Vialetto-van Laere syndrome 1
  • c.1073+16G>A Single submitter Brown-Vialetto-van Laere syndrome 1
  • c.1074-13T>G Single submitter Brown-Vialetto-van Laere syndrome 1
  • c.1074-15C>T Single submitter Brown-Vialetto-van Laere syndrome 1
  • c.1074-16C>G Single submitter Brown-Vialetto-van Laere syndrome 1
  • c.1074-16C>T Single submitter Brown-Vialetto-van Laere syndrome 1
  • c.1074-243T>C Single submitter
  • c.1074-275G>A Single submitter
  • c.1074-4C>A Single submitter Brown-Vialetto-van Laere syndrome 1
  • c.1074-50del Single submitter
  • c.1074-76C>T Single submitter
  • c.1074-8T>C Single submitter Brown-Vialetto-van Laere syndrome 1
  • c.1197+10C>T Single submitter Brown-Vialetto-van Laere syndrome 1
  • c.1197+13C>T Single submitter Brown-Vialetto-van Laere syndrome 1
  • c.1197+14C>G Single submitter Brown-Vialetto-van Laere syndrome 1
  • c.1197+15G>T Single submitter Brown-Vialetto-van Laere syndrome 1
  • c.1197+18G>A Single submitter Brown-Vialetto-van Laere syndrome 1
  • c.1198-10G>C Single submitter Brown-Vialetto-van Laere syndrome 1
  • c.1198-5C>G Single submitter Brown-Vialetto-van Laere syndrome 1
  • c.1198-6C>T Single submitter Brown-Vialetto-van Laere syndrome 1
  • c.1198-8C>A Single submitter Brown-Vialetto-van Laere syndrome 1
  • c.567+17G>A Single submitter Brown-Vialetto-van Laere syndrome 1
  • c.568-11G>A Single submitter Brown-Vialetto-van Laere syndrome 1
  • c.568-14C>G Single submitter Brown-Vialetto-van Laere syndrome 1
  • c.568-4G>T Single submitter Brown-Vialetto-van Laere syndrome 1
  • c.568-6T>C Single submitter Brown-Vialetto-van Laere syndrome 1
  • c.-3G>A Single submitter
  • c.*12A>G Single submitter
  • c.*13C>A Single submitter
  • c.*284G>A Single submitter
  • p.Ala156= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Ala158= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Ala188= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Ala338= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Ala428= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Ala435= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Ala460= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Ala469= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Arg132= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Arg266= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Arg422= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Arg65= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Asn257= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Asn94= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Asp101= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Asp186= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Asp258= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Asp272= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Cys10= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Cys166= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Cys409= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Cys432= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Gln242= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Glu171= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Glu26= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Glu36= Single submitter
  • p.Gly144= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Gly149= Single submitter
  • p.Gly15= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Gly286= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Gly330= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Gly374= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Gly418= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Gly433= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Gly443= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Gly54= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Gly82= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Ile106= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Ile187= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Ile265= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Ile303= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Ile48= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Leu100= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Leu111= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Leu138= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Leu147= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Leu199= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Leu209= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Leu221= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Leu235= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Leu255= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Leu318= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Leu361= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Leu405= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Leu421= Single submitter
  • p.Leu424= Single submitter
  • p.Leu430= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Leu442= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Leu456= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Leu57= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Leu61= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Leu7= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Leu79= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Lys414= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Phe108= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Phe12= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Phe126= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Phe3Leu Single submitter Inborn genetic diseases
  • p.Phe76= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Pro128= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Pro192= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Pro297= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Pro346= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Pro35= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Pro55= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Ser148= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Ser16= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Ser161= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Ser197= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Ser251= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Ser349= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Ser367= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Ser402= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Ser407= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Ser440= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Ser458= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Ser97= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Thr164= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Thr170= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Thr182= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Thr323= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Thr339= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Thr77= Single submitter
  • p.Thr96= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Tyr137= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Tyr213= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Val11= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Val18= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Val307= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Val351= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Val368= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Val400= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Val404= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Val413= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Val419= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Val420= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Val451= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Val453= Single submitter Brown-Vialetto-van Laere syndrome 1
  • p.Val58= Single submitter Brown-Vialetto-van Laere syndrome 1
  • c.-10A>C No assertion criteria SLC52A3-related disorder
  • c.-6A>C No assertion criteria SLC52A3-related disorder

Uncertain significance 220