SPP2 — 217 ClinVar variants
All ClinVar germline SPP2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 95 flagged for review →
1 Likely pathogenic · 10 Conflicting · 5 Benign · 3 Benign/Likely benign · 82 Likely benign · 116 Uncertain significance
Full SPP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 95
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 9
ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.
-
SPP2 p.Arg133His
Conflicting
Single submitter
inherited retinal dystrophy
- SPP2 p.Arg201Gln Conflicting Single submitter
-
SPP2 p.Arg93Lys
Conflicting
Single submitter
inherited retinal dystrophy
- SPP2 p.Asp42Glu Conflicting Single submitter
-
SPP2 p.Cys92Arg
Conflicting
Single submitter
inherited retinal dystrophy
-
SPP2 p.Pro58Leu
Conflicting
Single submitter
inherited retinal dystrophy
-
SPP2 p.Thr140Met
Conflicting
Single submitter
inherited retinal dystrophy
- SPP2 p.Thr9Met Conflicting Single submitter
-
SPP2 p.Tyr110Asp
Conflicting
Single submitter
inherited retinal dystrophy
Predictors lean, ClinVar uncertain 72
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- SPP2 p.Ala101Thr Uncertain significance Multiple submitters
- SPP2 p.Arg133Cys Uncertain significance Multiple submitters
- SPP2 p.Arg161Ile Uncertain significance Multiple submitters
- SPP2 p.Arg201Pro Uncertain significance Multiple submitters
- SPP2 p.Arg62Gln Uncertain significance Multiple submitters
- SPP2 p.Arg88Gln Uncertain significance Multiple submitters
- SPP2 p.Arg93Gly Uncertain significance Multiple submitters
- SPP2 p.Asn163Asp Uncertain significance Multiple submitters
- SPP2 p.Asn77Tyr Uncertain significance Multiple submitters
- SPP2 p.Cys27Tyr Uncertain significance Multiple submitters
- SPP2 p.Leu74Pro Uncertain significance Multiple submitters
- SPP2 p.Ser112Phe Uncertain significance Multiple submitters
- SPP2 p.Thr113Ile Uncertain significance Multiple submitters
- SPP2 p.Thr9Arg Uncertain significance Multiple submitters
- SPP2 p.Tyr179Cys Uncertain significance Multiple submitters
- SPP2 p.Ala114Pro Uncertain significance Single submitter
- SPP2 p.Ala124Val Uncertain significance Single submitter
- SPP2 p.Ala132Thr Uncertain significance Single submitter
- SPP2 p.Ala63Thr Uncertain significance Single submitter
- SPP2 p.Arg181Gln Uncertain significance Single submitter
- SPP2 p.Arg181Trp Uncertain significance Single submitter
- SPP2 p.Arg187Thr Uncertain significance Single submitter
- SPP2 p.Arg196Ser Uncertain significance Single submitter
- SPP2 p.Arg201Trp Uncertain significance Single submitter
- SPP2 p.Arg205Lys Uncertain significance Single submitter
- SPP2 p.Arg65Gly Uncertain significance Single submitter
- SPP2 p.Arg70Thr Uncertain significance Single submitter
- SPP2 p.Arg93Ser Uncertain significance Single submitter
- SPP2 p.Asn199Lys Uncertain significance Single submitter
- SPP2 p.Asn52Ile Uncertain significance Single submitter
- SPP2 p.Asn52Tyr Uncertain significance Single submitter
- SPP2 p.Asn78Asp Uncertain significance Single submitter
- SPP2 p.Asp108Val Uncertain significance Single submitter
- SPP2 p.Asp171Ala Uncertain significance Single submitter
- SPP2 p.Asp171Val Uncertain significance Single submitter
- SPP2 p.Asp34Asn Uncertain significance Single submitter
- SPP2 p.Asp36Asn Uncertain significance Single submitter
- SPP2 p.Asp42Asn Uncertain significance Single submitter
- SPP2 p.Cys92Tyr Uncertain significance Single submitter
- SPP2 p.Gln106Arg Uncertain significance Single submitter
- SPP2 p.Gln128Arg Uncertain significance Single submitter
- SPP2 p.Gln177Arg Uncertain significance Single submitter
- SPP2 p.Glu172Lys Uncertain significance Single submitter
- SPP2 p.Glu176Ala Uncertain significance Single submitter
- SPP2 p.Gly167Val Uncertain significance Single submitter
- SPP2 p.Ile14Thr Uncertain significance Single submitter
- SPP2 p.Ile174Val Uncertain significance Single submitter
- SPP2 p.Ile185Asn Uncertain significance Single submitter
- SPP2 p.Leu165Val Uncertain significance Single submitter
- SPP2 p.Leu168Val Uncertain significance Single submitter
- SPP2 p.Leu20Ile Uncertain significance Single submitter
- SPP2 p.Leu40Phe Uncertain significance Single submitter
- SPP2 p.Lys159Asn Uncertain significance Single submitter
- SPP2 p.Met10Lys Uncertain significance Single submitter
- SPP2 p.Met10Thr Uncertain significance Single submitter
- SPP2 p.Met17Thr Uncertain significance Single submitter
- SPP2 p.Met22Val Uncertain significance Single submitter
- SPP2 p.Pro191Leu Uncertain significance Single submitter
- SPP2 p.Pro192Leu Uncertain significance Single submitter
- SPP2 p.Ser112Tyr Uncertain significance Single submitter
- SPP2 p.Ser137Phe Uncertain significance Single submitter
- SPP2 p.Ser157Thr Uncertain significance Single submitter
- SPP2 p.Ser38Ala Uncertain significance Single submitter
- SPP2 p.Ser47Pro Uncertain significance Single submitter
- SPP2 p.Thr91Arg Uncertain significance Single submitter
- SPP2 p.Trp25Cys Uncertain significance Single submitter
- SPP2 p.Tyr164Cys Uncertain significance Single submitter
- SPP2 p.Tyr197His Uncertain significance Single submitter
- SPP2 p.Val115Leu Uncertain significance Single submitter
-
SPP2 p.Val120Met
Uncertain significance
Single submitter
inherited retinal dystrophy
- SPP2 p.Val32Ala Uncertain significance Single submitter
- SPP2 p.Val73Gly Uncertain significance Single submitter
Predictors split 14
The independent predictors disagree with each other — read with care.
- SPP2 p.Arg88Trp Uncertain significance Multiple submitters
- SPP2 p.Gln125Pro Uncertain significance Multiple submitters
- SPP2 p.Ser135Cys Uncertain significance Multiple submitters
- SPP2 p.Trp136Cys Uncertain significance Multiple submitters
- SPP2 p.Val127Met Uncertain significance Multiple submitters
- SPP2 p.Val130Met Uncertain significance Multiple submitters
- SPP2 p.Arg133Pro Uncertain significance Single submitter
- SPP2 p.Arg62Trp Uncertain significance Single submitter
- SPP2 p.Asp99Tyr Uncertain significance Single submitter
- SPP2 p.Leu20His Uncertain significance Single submitter
- SPP2 p.Met81Ile Uncertain significance Single submitter
- SPP2 p.Ser53Cys Uncertain significance Single submitter
- SPP2 p.Trp136Arg Uncertain significance Single submitter
-
SPP2 p.Val71Ala
Conflicting
Single submitter
inherited retinal dystrophy
All SPP2 variants
Likely pathogenic 1
- p.Phe18fs Single submitter inherited retinal dystrophy
Conflicting classifications of pathogenicity 10
- p.Arg133His Single submitter inherited retinal dystrophy ⚠
- p.Arg201Gln Single submitter ⚠
- p.Arg93Lys Single submitter inherited retinal dystrophy ⚠
- p.Asp42Glu Single submitter ⚠
- p.Cys92Arg Single submitter inherited retinal dystrophy ⚠
- p.Pro58Leu Single submitter inherited retinal dystrophy ⚠
- p.Thr140Met Single submitter inherited retinal dystrophy ⚠
- p.Thr9Met Single submitter ⚠
- p.Tyr110Asp Single submitter inherited retinal dystrophy ⚠
- p.Val71Ala Single submitter inherited retinal dystrophy ⚠
Benign 5
- p.Asp36Glu Multiple submitters inherited retinal dystrophy
- p.Pro100= Multiple submitters
- p.Thr90= Multiple submitters inherited retinal dystrophy
- c.*1C>T Single submitter inherited retinal dystrophy
- p.Leu60Val Single submitter inherited retinal dystrophy
Benign/Likely benign 3
- c.444+16dup Multiple submitters
- c.*2G>A Multiple submitters inherited retinal dystrophy
- p.Gly129= Multiple submitters
Likely benign 82
- c.210+7G>T Multiple submitters
- c.211-15T>C Multiple submitters
- c.333+12G>A Multiple submitters
- c.499+16T>G Multiple submitters
- c.499+7T>G Multiple submitters
- c.86-14G>C Multiple submitters
- c.86-14G>T Multiple submitters
- c.86-8G>A Multiple submitters
- c.86-9C>T Multiple submitters
- p.Ala124= Multiple submitters
- p.Ala204Ser Multiple submitters
- p.Arg41= Multiple submitters
- p.Asp36= Multiple submitters
- p.Ile16= Multiple submitters
- p.Leu60= Multiple submitters
- p.Phe151Ser Multiple submitters
- p.Pro58= Multiple submitters
- p.Ser38Phe Multiple submitters
- p.Thr113= Multiple submitters
- p.Thr119= Multiple submitters
- p.Thr9= Multiple submitters
- c.210+11A>T Single submitter
- c.210+13T>G Single submitter
- c.210+17A>G Single submitter
- c.210+19C>T Single submitter
- c.210+7G>A Single submitter
- c.211-16C>A Single submitter
- c.211-18A>C Single submitter
- c.211-20G>A Single submitter
- c.333+11G>A Single submitter
- c.333+16C>T Single submitter
- c.334-18C>T Single submitter
- c.334-20C>T Single submitter
- c.444+14del Single submitter
- c.444+17G>A Single submitter
- c.444+7C>A Single submitter
- c.445-12G>A Single submitter
- c.445-13T>C Single submitter
- c.445-15C>T Single submitter
- c.445-20T>C Single submitter
- c.499+10G>A Single submitter
- c.499+13C>T Single submitter
- c.500-4A>G Single submitter
- c.550+14T>C Single submitter
- c.550+16C>A Single submitter
- c.551-13T>C Single submitter
- c.551-6C>T Single submitter
- c.551-9T>C Single submitter
- c.85+13C>A Single submitter
- c.85+19T>C Single submitter
- c.85+20G>A Single submitter
- c.86-5T>C Single submitter
- c.-1C>A Single submitter
- p.Ala63= Single submitter
- p.Arg4= Single submitter
- p.Arg62= Single submitter
- p.Arg93= Single submitter
- p.Asn23= Single submitter
- p.Asp171= Single submitter
- p.Asp42= Single submitter
- p.Ile169= Single submitter
- p.Ile206= Single submitter
- p.Leu155= Single submitter
- p.Leu165= Single submitter
- p.Leu168= Single submitter
- p.Leu44= Single submitter
- p.Phe61= Single submitter
- p.Ser135= Single submitter
- p.Ser137= Single submitter
- p.Ser139= Single submitter
- p.Ser146= Single submitter
- p.Ser175= Single submitter
- p.Ser55= Single submitter
- p.Thr140= Single submitter
- p.Thr91= Single submitter
- p.Tyr164= Single submitter
- p.Tyr24= Single submitter
- p.Tyr33= Single submitter
- p.Tyr35= Single submitter inherited retinal dystrophy
- p.Val122= Single submitter
- p.Val32= Single submitter
- p.Val48= Single submitter
Uncertain significance 116
- c.210+1G>A Multiple submitters
- c.500-1G>T Multiple submitters
- c.86-1G>T Multiple submitters
- p.Ala101Thr Multiple submitters ⚠
- p.Arg133Cys Multiple submitters ⚠
- p.Arg161Ile Multiple submitters ⚠
- p.Arg201Pro Multiple submitters ⚠
- p.Arg62Gln Multiple submitters ⚠
- p.Arg88Gln Multiple submitters ⚠
- p.Arg88Trp Multiple submitters ⚠
- p.Arg93Gly Multiple submitters ⚠
- p.Asn163Asp Multiple submitters ⚠
- p.Asn77Tyr Multiple submitters ⚠
- p.Cys27Tyr Multiple submitters ⚠
- p.Gln125Pro Multiple submitters ⚠
- p.Gln125Ter Multiple submitters
- p.Gln177_Tyr179delinsHis Multiple submitters
- p.Leu74Pro Multiple submitters ⚠
- p.Ser112Phe Multiple submitters ⚠
- p.Ser135Cys Multiple submitters ⚠
- p.Thr113Ile Multiple submitters ⚠
- p.Thr9Arg Multiple submitters ⚠
- p.Trp136Cys Multiple submitters ⚠
- p.Tyr179Cys Multiple submitters ⚠
- p.Tyr197Ter Multiple submitters inherited retinal dystrophy
- p.Val127Met Multiple submitters ⚠
- p.Val130Met Multiple submitters ⚠
- c.210+2T>G Single submitter
- c.333+1G>A Single submitter
- c.333+1G>C Single submitter
- c.444+1G>T Single submitter
- c.500-6T>C Single submitter
- c.500-8T>C Single submitter
- c.550+1G>A Single submitter
- c.550+2T>G Single submitter
- c.86-9C>A Single submitter
- p.Ala114Pro Single submitter ⚠
- p.Ala124Val Single submitter ⚠
- p.Ala132Thr Single submitter ⚠
- p.Ala63Thr Single submitter ⚠
- p.Arg133Pro Single submitter ⚠
- p.Arg181= Single submitter
- p.Arg181Gln Single submitter ⚠
- p.Arg181Trp Single submitter ⚠
- p.Arg187Thr Single submitter ⚠
- p.Arg195Ter Single submitter
- p.Arg196Ser Single submitter ⚠
- p.Arg201Trp Single submitter ⚠
- p.Arg205Lys Single submitter ⚠
- p.Arg62Gly Single submitter inherited retinal dystrophy
- p.Arg62Trp Single submitter ⚠
- p.Arg65Gly Single submitter ⚠
- p.Arg70Thr Single submitter ⚠
- p.Arg93Ser Single submitter ⚠
- p.Asn162fs Single submitter
- p.Asn199Lys Single submitter ⚠
- p.Asn52Ile Single submitter ⚠
- p.Asn52Tyr Single submitter ⚠
- p.Asn78Asp Single submitter ⚠
- p.Asp108Val Single submitter ⚠
- p.Asp171Ala Single submitter ⚠
- p.Asp171Val Single submitter ⚠
- p.Asp34Asn Single submitter ⚠
- p.Asp36Asn Single submitter ⚠
- p.Asp42Asn Single submitter ⚠
- p.Asp99Gly Single submitter
- p.Asp99Tyr Single submitter ⚠
- p.Cys92Tyr Single submitter ⚠
- p.Gln106Arg Single submitter ⚠
- p.Gln128Arg Single submitter ⚠
- p.Gln128Ter Single submitter inherited retinal dystrophy
- p.Gln177Arg Single submitter ⚠
- p.Gln54Ter Single submitter
- p.Glu147Lys Single submitter
- p.Glu172Lys Single submitter ⚠
- p.Glu176Ala Single submitter ⚠
- p.Gly167Val Single submitter ⚠
- p.Gly21_Asn23del Single submitter
- p.Ile14Thr Single submitter ⚠
- p.Ile174Val Single submitter ⚠
- p.Ile185Asn Single submitter ⚠
- p.Leu165Val Single submitter ⚠
- p.Leu168Val Single submitter ⚠
- p.Leu20His Single submitter ⚠
- p.Leu20Ile Single submitter ⚠
- p.Leu40Phe Single submitter ⚠
- p.Lys159Asn Single submitter ⚠
- p.Met10Lys Single submitter ⚠
- p.Met10Thr Single submitter ⚠
- p.Met17Thr Single submitter ⚠
- p.Met22Val Single submitter ⚠
- p.Met81Ile Single submitter ⚠
- p.Pro191Leu Single submitter ⚠
- p.Pro192Leu Single submitter ⚠
- p.Ser112Tyr Single submitter ⚠
- p.Ser135fs Single submitter
- p.Ser137Phe Single submitter ⚠
- p.Ser146Gly Single submitter
- p.Ser157Thr Single submitter ⚠
- p.Ser28= Single submitter
- p.Ser38Ala Single submitter ⚠
- p.Ser47Pro Single submitter ⚠
- p.Ser53Cys Single submitter ⚠
- p.Thr91Arg Single submitter ⚠
- p.Trp136Arg Single submitter ⚠
- p.Trp25_Ser26delinsCysPro Single submitter
- p.Trp25Cys Single submitter ⚠
- p.Tyr164Cys Single submitter ⚠
- p.Tyr197fs Single submitter
- p.Tyr197His Single submitter ⚠
- p.Tyr24_Trp25insValCysSerTrpAsnTyrVal Single submitter
- p.Tyr59Ter Single submitter
- p.Val115Leu Single submitter ⚠
- p.Val120Met Single submitter inherited retinal dystrophy ⚠
- p.Val32Ala Single submitter ⚠
- p.Val73Gly Single submitter ⚠