SPATA7 — 510 ClinVar variants

All ClinVar germline SPATA7 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 251 flagged for review →

36 Pathogenic · 11 Pathogenic/Likely pathogenic · 25 Likely pathogenic · 32 Conflicting · 10 Benign · 12 Benign/Likely benign · 118 Likely benign · 266 Uncertain significance

Full SPATA7 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 251

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 15

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

Predictors lean, ClinVar uncertain 201

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 201

Predictors split 35

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

All SPATA7 variants

Pathogenic 36

  • p.Glu99fs Multiple submitters Leber congenital amaurosis 3
  • p.Lys163Ter Multiple submitters inherited retinal dystrophy
  • p.Phe233_Ser234insTer Multiple submitters Leber congenital amaurosis
  • p.Pro321fs Multiple submitters Paediatric disorders
  • p.Ser39fs Multiple submitters Leber congenital amaurosis 3
  • p.Thr375_Asp376insTer Multiple submitters Leber congenital amaurosis 3
  • p.Val458fs Multiple submitters Leber congenital amaurosis 3
  • c.1161-1G>C Single submitter Leber congenital amaurosis 3
  • c.1161-2A>G Single submitter Leber congenital amaurosis 3
  • c.845+1G>A Single submitter inherited retinal dystrophy
  • c.901_912+1del Single submitter Leber congenital amaurosis 3
  • c.(912+1_913-1 Single submitter inherited retinal dystrophy
  • p.Gln130Ter Single submitter Leber congenital amaurosis 3
  • p.Gln399Ter Single submitter Leber congenital amaurosis 3
  • p.Glu315Ter Single submitter Leber congenital amaurosis 3
  • p.Glu364Ter Single submitter Leber congenital amaurosis 3
  • p.Glu404Ter Single submitter Leber congenital amaurosis 3
  • p.Gly324fs Single submitter Leber congenital amaurosis 3
  • p.Leu161fs Single submitter Leber congenital amaurosis 3
  • p.Leu366fs Single submitter Leber congenital amaurosis 3
  • p.Met140fs Single submitter Leber congenital amaurosis 3
  • p.Met408fs Single submitter Leber congenital amaurosis 3
  • p.Met473fs Single submitter Leber congenital amaurosis 3
  • p.Ser195fs Single submitter Leber congenital amaurosis 3
  • p.Ser234fs Single submitter Leber congenital amaurosis 3
  • p.Ser354fs Single submitter Leber congenital amaurosis 3
  • p.Thr247fs Single submitter SPATA7-related disorder
  • p.Thr289fs Single submitter Leber congenital amaurosis 3
  • p.Tyr359_Ser360insTer Single submitter Leber congenital amaurosis 3
  • p.Tyr56_Asn57delinsTer Single submitter Leber congenital amaurosis 3
  • c.19+1G>C No assertion criteria Leber congenital amaurosis 3
  • c.(?_-175 No assertion criteria Leber congenital amaurosis 3
  • p.Gln255Ter No assertion criteria Leber congenital amaurosis 3
  • p.Glu405Asp No assertion criteria Leber congenital amaurosis ⚠
  • p.Ile302fs No assertion criteria Leber congenital amaurosis 3
  • p.Tyr199fs No assertion criteria inherited retinal dystrophy

Pathogenic/Likely pathogenic 11

  • c.19+2T>A Multiple submitters SPATA7-related disorder
  • p.Arg108Ter Multiple submitters SPATA7-related disorder
  • p.Arg391Ter Multiple submitters retinitis pigmentosa
  • p.Arg395Ter Multiple submitters SPATA7-related disorder
  • p.Arg85Ter Multiple submitters SPATA7-related disorder
  • p.Asn400fs Multiple submitters SPATA7-related disorder
  • p.Asp270fs Multiple submitters Leber congenital amaurosis 3
  • p.Cys96Ter Multiple submitters SPATA7-related disorder
  • p.Leu368fs Multiple submitters SPATA7-related disorder
  • p.Leu89fs Multiple submitters SPATA7-related disorder
  • p.Ser75fs Multiple submitters SPATA7-related disorder

Likely pathogenic 25

Conflicting classifications of pathogenicity 32

Benign 10

Benign/Likely benign 12

  • c.1215+7C>A Multiple submitters Leber congenital amaurosis 3
  • c.190+16T>C Multiple submitters Leber congenital amaurosis 3
  • p.Arg534Gln Multiple submitters Leber congenital amaurosis 3
  • p.Gln95Arg Multiple submitters retinitis pigmentosa
  • p.Gly127= Multiple submitters Leber congenital amaurosis 3
  • p.Gly324Glu Multiple submitters Leber congenital amaurosis 3
  • p.Leu122Phe Multiple submitters Leber congenital amaurosis 3
  • p.Phe119Leu Multiple submitters Leber congenital amaurosis 3
  • p.Ser115= Multiple submitters Leber congenital amaurosis 3
  • p.Ser165Asn Multiple submitters Leber congenital amaurosis 3
  • p.Ser340= Multiple submitters Leber congenital amaurosis 3
  • p.Val74Met Multiple submitters inherited retinal dystrophy

Likely benign 118

  • c.1083-17T>C Multiple submitters Leber congenital amaurosis 3
  • c.1161-9C>T Multiple submitters Leber congenital amaurosis 3
  • c.1216-19C>T Multiple submitters Leber congenital amaurosis 3
  • c.190+14A>G Multiple submitters Leber congenital amaurosis 3
  • c.372+7T>G Multiple submitters Leber congenital amaurosis 3
  • c.373-16T>C Multiple submitters Leber congenital amaurosis 3
  • c.846-6T>C Multiple submitters Leber congenital amaurosis 3
  • c.912+8G>A Multiple submitters Leber congenital amaurosis 3
  • p.Asn170= Multiple submitters Leber congenital amaurosis 3
  • p.Asp575Asn Multiple submitters Leber congenital amaurosis 3
  • p.Gln278= Multiple submitters Leber congenital amaurosis 3
  • p.Glu362= Multiple submitters
  • p.Gly189= Multiple submitters Leber congenital amaurosis 3
  • p.Leu415= Multiple submitters Leber congenital amaurosis 3
  • p.Phe393= Multiple submitters Leber congenital amaurosis 3
  • p.Pro180= Multiple submitters Leber congenital amaurosis 3
  • p.Pro190= Multiple submitters Leber congenital amaurosis 3
  • p.Ser149= Multiple submitters Leber congenital amaurosis 3
  • p.Ser188= Multiple submitters Leber congenital amaurosis 3
  • p.Ser218Leu Multiple submitters Leber congenital amaurosis 3
  • p.Ser254= Multiple submitters Leber congenital amaurosis 3
  • p.Ser570= Multiple submitters Leber congenital amaurosis 3
  • p.Thr241= Multiple submitters Leber congenital amaurosis 3
  • p.Val438= Multiple submitters Leber congenital amaurosis 3
  • c.1083-10_1083-7del Single submitter Leber congenital amaurosis 3
  • c.1083-12T>C Single submitter Leber congenital amaurosis 3
  • c.1083-15G>A Single submitter Leber congenital amaurosis 3
  • c.1160+18T>C Single submitter Leber congenital amaurosis 3
  • c.1161-16T>C Single submitter Leber congenital amaurosis 3
  • c.1161-8A>G Single submitter Leber congenital amaurosis 3
  • c.1215+12C>T Single submitter Leber congenital amaurosis 3
  • c.1215+14T>C Single submitter Leber congenital amaurosis 3
  • c.1215+7C>T Single submitter Leber congenital amaurosis 3
  • c.1216-17T>C Single submitter Leber congenital amaurosis 3
  • c.1216-20T>G Single submitter Leber congenital amaurosis 3
  • c.1216-4del Single submitter Leber congenital amaurosis 3
  • c.19+20G>A Single submitter Leber congenital amaurosis 3
  • c.190+11G>A Single submitter Leber congenital amaurosis 3
  • c.190+12C>A Single submitter Leber congenital amaurosis 3
  • c.191-14C>T Single submitter Leber congenital amaurosis 3
  • c.20-12T>C Single submitter Leber congenital amaurosis 3
  • c.20-14T>C Single submitter
  • c.20-18_20-17insC Single submitter Leber congenital amaurosis 3
  • c.20-8G>T Single submitter Leber congenital amaurosis 3
  • c.20-9T>C Single submitter Leber congenital amaurosis 3
  • c.238+17C>T Single submitter Leber congenital amaurosis 3
  • c.238+19T>C Single submitter
  • c.238+7A>G Single submitter Leber congenital amaurosis 3
  • c.239-14G>T Single submitter Leber congenital amaurosis 3
  • c.239-19G>T Single submitter Leber congenital amaurosis 3
  • c.372+10T>G Single submitter Leber congenital amaurosis 3
  • c.372+9G>A Single submitter Leber congenital amaurosis 3
  • c.373-12G>A Single submitter Leber congenital amaurosis 3
  • c.845+9C>T Single submitter Leber congenital amaurosis 3
  • c.912+10A>G Single submitter Leber congenital amaurosis 3
  • c.912+17C>A Single submitter
  • c.913-15T>G Single submitter Leber congenital amaurosis 3
  • c.94+19A>G Single submitter Leber congenital amaurosis 3
  • c.94+6dup Single submitter Leber congenital amaurosis 3
  • c.94+8A>G Single submitter Leber congenital amaurosis 3
  • c.95-19A>G Single submitter Leber congenital amaurosis 3
  • p.Ala220= Single submitter Leber congenital amaurosis 3
  • p.Ala305= Single submitter Leber congenital amaurosis 3
  • p.Ala318= Single submitter Leber congenital amaurosis 3
  • p.Ala81= Single submitter Leber congenital amaurosis 3
  • p.Arg108= Single submitter Leber congenital amaurosis 3
  • p.Arg156= Single submitter Leber congenital amaurosis 3
  • p.Arg257= Single submitter Leber congenital amaurosis 3
  • p.Arg86= Single submitter Leber congenital amaurosis 3
  • p.Asp544= Single submitter Leber congenital amaurosis 3
  • p.Asp579= Single submitter Leber congenital amaurosis 3
  • p.Cys34= Single submitter Leber congenital amaurosis 3
  • p.Gln130= Single submitter Leber congenital amaurosis 3
  • p.Gln430= Single submitter Leber congenital amaurosis 3
  • p.Gln83= Single submitter
  • p.Gln84= Single submitter Leber congenital amaurosis 3
  • p.Glu404= Single submitter Leber congenital amaurosis 3
  • p.Glu425= Single submitter Leber congenital amaurosis 3
  • p.Glu535= Single submitter Leber congenital amaurosis 3
  • p.Gly288= Single submitter Leber congenital amaurosis 3
  • p.Gly382= Single submitter
  • p.Gly574= Single submitter Leber congenital amaurosis 3
  • p.His413= Single submitter Leber congenital amaurosis 3
  • p.Ile397= Single submitter Leber congenital amaurosis 3
  • p.Ile59= Single submitter Leber congenital amaurosis 3
  • p.Leu150= Single submitter Leber congenital amaurosis 3
  • p.Leu157= Single submitter Leber congenital amaurosis 3
  • p.Leu159= Single submitter
  • p.Leu198= Single submitter Leber congenital amaurosis 3
  • p.Leu21= Single submitter Leber congenital amaurosis 3
  • p.Leu287= Single submitter Leber congenital amaurosis 3
  • p.Leu365= Single submitter Leber congenital amaurosis 3
  • p.Leu419= Single submitter Leber congenital amaurosis 3
  • p.Leu436= Single submitter Leber congenital amaurosis 3
  • p.Leu475= Single submitter Leber congenital amaurosis 3
  • p.Leu515= Single submitter Leber congenital amaurosis 3
  • p.Lys174= Single submitter Leber congenital amaurosis 3
  • p.Pro172= Single submitter Leber congenital amaurosis 3
  • p.Pro596= Single submitter Leber congenital amaurosis 3
  • p.Ser178= Single submitter Leber congenital amaurosis 3
  • p.Ser210= Single submitter Leber congenital amaurosis 3
  • p.Ser218= Single submitter Leber congenital amaurosis 3
  • p.Ser341= Single submitter Leber congenital amaurosis 3
  • p.Ser385= Single submitter Leber congenital amaurosis 3
  • p.Ser73= Single submitter Leber congenital amaurosis 3
  • p.Thr169= Single submitter Leber congenital amaurosis 3
  • p.Thr206= Single submitter Leber congenital amaurosis 3
  • p.Thr277= Single submitter Leber congenital amaurosis 3
  • p.Thr279= Single submitter Leber congenital amaurosis 3
  • p.Thr292Ile Single submitter Inborn genetic diseases
  • p.Thr310= Single submitter Leber congenital amaurosis 3
  • p.Thr422= Single submitter Leber congenital amaurosis 3
  • p.Thr489= Single submitter Leber congenital amaurosis 3
  • p.Tyr199= Single submitter Leber congenital amaurosis 3
  • p.Tyr259= Single submitter Leber congenital amaurosis 3
  • p.Val12= Single submitter Leber congenital amaurosis 3
  • p.Val428= Single submitter Leber congenital amaurosis 3
  • c.1029-10_1029-4del No assertion criteria SPATA7-related disorder

Uncertain significance 266