IFT52 — 229 ClinVar variants
All ClinVar germline IFT52 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 72 flagged for review →
5 Pathogenic · 1 Pathogenic/Likely pathogenic · 2 Likely pathogenic · 3 Conflicting · 27 Benign · 3 Benign/Likely benign · 100 Likely benign · 88 Uncertain significance
Full IFT52 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 72
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.
-
IFT52 p.Asn98Ser
Pathogenic
No assertion criteria
short-rib thoracic dysplasia 16 with or without polydactyly
Predictors agree, ClinVar conflicts 2
ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.
Predictors lean, ClinVar uncertain 48
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- IFT52 p.Asn35Ser Uncertain significance Multiple submitters
- IFT52 p.Glu4Asp Uncertain significance Multiple submitters
- IFT52 p.Gly134Glu Uncertain significance Multiple submitters
- IFT52 p.Ala161Val Uncertain significance Single submitter
- IFT52 p.Ala309Val Uncertain significance Single submitter
- IFT52 p.Ala68Pro Uncertain significance Single submitter
- IFT52 p.Arg142Gln Uncertain significance Single submitter
- IFT52 p.Arg272Gln Uncertain significance Single submitter
- IFT52 p.Arg272Trp Uncertain significance Single submitter
- IFT52 p.Arg33Trp Uncertain significance Single submitter
- IFT52 p.Asn118Lys Uncertain significance Single submitter
- IFT52 p.Asn22Thr Uncertain significance Single submitter
- IFT52 p.Asp244Gly Uncertain significance Single submitter
- IFT52 p.Asp281Glu Uncertain significance Single submitter
- IFT52 p.Cys190Ser Uncertain significance Single submitter
- IFT52 p.Glu275Gly Uncertain significance Single submitter
- IFT52 p.Glu279Gln Uncertain significance Single submitter
- IFT52 p.Glu308Asp Uncertain significance Single submitter
- IFT52 p.Glu311Gly Uncertain significance Single submitter
-
IFT52 p.Glu311Lys
Uncertain significance
Single submitter
Jeune syndrome
- IFT52 p.Glu48Asp Uncertain significance Single submitter
- IFT52 p.Glu92Gly Uncertain significance Single submitter
- IFT52 p.Gly243Arg Uncertain significance Single submitter
- IFT52 p.His217Tyr Uncertain significance Single submitter
- IFT52 p.Ile152Thr Uncertain significance Single submitter
- IFT52 p.Ile18Thr Uncertain significance Single submitter
- IFT52 p.Ile283Val Uncertain significance Single submitter
- IFT52 p.Ile295Val Uncertain significance Single submitter
- IFT52 p.Ile406Thr Uncertain significance Single submitter
- IFT52 p.Leu334Phe Uncertain significance Single submitter
- IFT52 p.Leu351Met Uncertain significance Single submitter
- IFT52 p.Lys127Thr Uncertain significance Single submitter
- IFT52 p.Met28Val Uncertain significance Single submitter
- IFT52 p.Ser230Cys Uncertain significance Single submitter
- IFT52 p.Ser40Arg Uncertain significance Single submitter
- IFT52 p.Ser429Asn Uncertain significance Single submitter
- IFT52 p.Thr186Ile Uncertain significance Single submitter
- IFT52 p.Thr241Met Uncertain significance Single submitter
- IFT52 p.Thr333Asn Uncertain significance Single submitter
- IFT52 p.Thr359Met Uncertain significance Single submitter
- IFT52 p.Thr66Ala Uncertain significance Single submitter
- IFT52 p.Thr97Ile Uncertain significance Single submitter
- IFT52 p.Tyr76Cys Uncertain significance Single submitter
- IFT52 p.Val116Ile Uncertain significance Single submitter
- IFT52 p.Val119Ala Uncertain significance Single submitter
- IFT52 p.Val306Ile Uncertain significance Single submitter
- IFT52 p.Val410Ile Uncertain significance Single submitter
- IFT52 p.Val415Met Uncertain significance Single submitter
Predictors split 21
The independent predictors disagree with each other — read with care.
- IFT52 p.Leu164Phe Uncertain significance Multiple submitters
- IFT52 p.Phe95Ser Uncertain significance Multiple submitters
-
IFT52 p.Pro397Ser
Uncertain significance
Multiple submitters
short-rib thoracic dysplasia 16 with or without polydactyly
-
IFT52 p.Val53Met
Uncertain significance
Multiple submitters
short-rib thoracic dysplasia 16 with or without polydactyly
- IFT52 p.Ala182Val Uncertain significance Single submitter
- IFT52 p.Ala337Val Uncertain significance Single submitter
- IFT52 p.Arg344Trp Uncertain significance Single submitter
- IFT52 p.Arg6Trp Uncertain significance Single submitter
- IFT52 p.Asp402Val Uncertain significance Single submitter
- IFT52 p.Gln222Arg Uncertain significance Single submitter
- IFT52 p.Glu63Gly Uncertain significance Single submitter
- IFT52 p.Gly187Ala Uncertain significance Single submitter
- IFT52 p.Gly80Ser Uncertain significance Single submitter
- IFT52 p.Leu290Phe Uncertain significance Single submitter
- IFT52 p.Leu322Phe Uncertain significance Single submitter
- IFT52 p.Leu356Phe Uncertain significance Single submitter
- IFT52 p.Met86Ile Uncertain significance Single submitter
- IFT52 p.Phe191Leu Uncertain significance Single submitter
- IFT52 p.Phe381Leu Uncertain significance Single submitter
- IFT52 p.Pro330Leu Uncertain significance Single submitter
-
IFT52 p.Thr186Ala
Pathogenic
No assertion criteria
short-rib thoracic dysplasia 16 with or without polydactyly
All IFT52 variants
Pathogenic 5
- p.Arg142Ter Single submitter short-rib thoracic dysplasia 16 with or without polydactyly
- p.Arg274Ter Single submitter
- p.Asn98Ser No assertion criteria short-rib thoracic dysplasia 16 with or without polydactyly ⚠
- p.Ile232_Met233delinsThr No assertion criteria short-rib thoracic dysplasia 16 with or without polydactyly
- p.Thr186Ala No assertion criteria short-rib thoracic dysplasia 16 with or without polydactyly ⚠
Pathogenic/Likely pathogenic 1
- p.Leu293fs No assertion criteria short-rib thoracic dysplasia 16 with or without polydactyly
Likely pathogenic 2
- p.Ala199Thr Single submitter short-rib thoracic dysplasia 16 with or without polydactyly
- p.Trp239Ter Single submitter short-rib thoracic dysplasia 16 with or without polydactyly
Conflicting classifications of pathogenicity 3
- c.338-3T>A Single submitter
- p.Arg344Gln Single submitter ⚠
- p.Asp427Asn Single submitter ⚠
Benign 27
- c.1011+73T>C Multiple submitters
- c.1012-135A>G Multiple submitters
- c.1012-85T>C Multiple submitters
- c.1120+73G>A Multiple submitters
- c.1121-198T>C Multiple submitters
- c.1267-77G>T Multiple submitters
- c.486-38T>A Multiple submitters
- c.612+84C>T Multiple submitters
- c.700-8dup Multiple submitters
- c.700-99C>T Multiple submitters
- c.924-64G>A Multiple submitters
- p.Ala337= Multiple submitters
- p.Glu275= Multiple submitters
- p.Leu174= Multiple submitters
- p.Tyr201Cys Multiple submitters
- p.Val53= Multiple submitters short-rib thoracic dysplasia 16 with or without polydactyly
- c.1012-3del Single submitter
- c.119+232C>G Single submitter
- c.1266+110T>G Single submitter
- c.1266+15A>G Single submitter
- c.337+125C>G Single submitter
- c.486-134C>A Single submitter
- c.699+140C>T Single submitter
- c.700-10_700-8dup Single submitter
- c.700-6dup Single submitter
- c.769-206G>T Single submitter
- p.Leu269= Single submitter
Benign/Likely benign 3
- c.1120+26del Multiple submitters
- c.1120+26dup Multiple submitters
- c.700-9_700-8dup Multiple submitters
Likely benign 100
- c.1121-11A>T Multiple submitters
- c.119+11A>T Multiple submitters
- c.119+5C>T Multiple submitters
- p.Gln206= Multiple submitters
- c.1012-13dup Single submitter
- c.1012-20A>G Single submitter
- c.1120+11C>G Single submitter
- c.1120+11C>T Single submitter
- c.1120+20T>C Single submitter
- c.1121-13C>A Single submitter
- c.1121-4T>C Single submitter
- c.119+11A>G Single submitter
- c.119+15A>G Single submitter
- c.119+20G>A Single submitter
- c.120-10G>A Single submitter
- c.120-5T>C Single submitter
- c.1266+18C>T Single submitter
- c.1267-13T>C Single submitter
- c.1267-19G>C Single submitter
- c.1267-7C>T Single submitter
- c.207+15C>T Single submitter
- c.208-18C>T Single submitter
- c.337+11T>G Single submitter
- c.337+13A>C Single submitter
- c.337+14T>C Single submitter
- c.337+20T>C Single submitter
- c.337+8G>A Single submitter
- c.337+8G>T Single submitter
- c.338-17C>G Single submitter
- c.338-18T>C Single submitter
- c.413+19G>A Single submitter
- c.413+5G>A Single submitter
- c.414-12T>C Single submitter
- c.486-10T>C Single submitter
- c.612+18T>C Single submitter
- c.613-18C>T Single submitter
- c.613-4A>G Single submitter
- c.700-15_700-14insC Single submitter
- c.700-18_700-17insA Single submitter
- c.700-8T>A Single submitter
- c.768+10G>A Single submitter
- c.768+9del Single submitter
- c.769-12_769-11insTGTGAAAGCCTCTT Single submitter
- c.923+10T>A Single submitter
- c.923+6T>C Single submitter
- c.923+7A>G Single submitter
- p.Ala13= Single submitter
- p.Ala163= Single submitter
- p.Ala182= Single submitter
- p.Ala252= Single submitter
- p.Ala67= Single submitter
- p.Arg272= Single submitter
- p.Arg33= Single submitter
- p.Asn111= Single submitter
- p.Asn194= Single submitter
- p.Asn23= Single submitter
- p.Asn436= Single submitter
- p.Asp259His Single submitter
- p.Cys386= Single submitter
- p.Glu282Lys Single submitter
- p.Glu311= Single submitter
- p.Glu4= Single submitter
- p.His409= Single submitter
- p.Ile426= Single submitter
- p.Ile45= Single submitter
- p.Ile72= Single submitter
- p.Ile99= Single submitter
- p.Leu103= Single submitter
- p.Leu322= Single submitter
- p.Leu353= Single submitter
- p.Leu41= Single submitter
- p.Leu73= Single submitter
- p.Leu87= Single submitter
- p.Lys418= Single submitter
- p.Lys419= Single submitter
- p.Lys75= Single submitter
- p.Phe291= Single submitter
- p.Phe411= Single submitter
- p.Phe437= Single submitter
- p.Pro192= Single submitter
- p.Pro284= Single submitter
- p.Pro330= Single submitter
- p.Pro350Leu Single submitter
- p.Ser294= Single submitter
- p.Ser305= Single submitter
- p.Thr20= Single submitter
- p.Thr21= Single submitter
- p.Thr241= Single submitter
- p.Thr333= Single submitter
- p.Thr333Ala Single submitter
- p.Thr393= Single submitter
- p.Thr431= Single submitter
- p.Thr97= Single submitter
- p.Tyr14= Single submitter
- p.Tyr382= Single submitter
- p.Val115= Single submitter
- p.Val167= Single submitter
- p.Val236= Single submitter
- p.Val306= Single submitter
- p.Ile307= No assertion criteria IFT52-related disorder
Uncertain significance 88
- p.Asn35Ser Multiple submitters ⚠
- p.Glu4Asp Multiple submitters ⚠
- p.Gly134Glu Multiple submitters ⚠
- p.Ile99fs Multiple submitters
- p.Leu164Phe Multiple submitters ⚠
- p.Leu334Arg Multiple submitters
- p.Phe95Ser Multiple submitters ⚠
- p.Pro397Ser Multiple submitters short-rib thoracic dysplasia 16 with or without polydactyly ⚠
- p.Val53Met Multiple submitters short-rib thoracic dysplasia 16 with or without polydactyly ⚠
- c.1012-3T>C Single submitter
- c.208-3T>A Single submitter
- c.413+5del Single submitter
- c.414-9T>G Single submitter
- c.613-128_622del Single submitter
- c.700-3T>G Single submitter
- c.-27G>C Single submitter
- p.Ala144fs Single submitter
- p.Ala161Val Single submitter ⚠
- p.Ala182fs Single submitter
- p.Ala182Val Single submitter ⚠
- p.Ala309Val Single submitter ⚠
- p.Ala337Val Single submitter ⚠
- p.Ala68Pro Single submitter ⚠
- p.Arg142Gln Single submitter ⚠
- p.Arg272Gln Single submitter ⚠
- p.Arg272Trp Single submitter ⚠
- p.Arg33Trp Single submitter ⚠
- p.Arg344Trp Single submitter ⚠
- p.Arg6Trp Single submitter ⚠
- p.Asn118Lys Single submitter ⚠
- p.Asn22Thr Single submitter ⚠
- p.Asp234Val Single submitter
- p.Asp244fs Single submitter
- p.Asp244Gly Single submitter ⚠
- p.Asp254Gly Single submitter
- p.Asp281Glu Single submitter ⚠
- p.Asp402Val Single submitter ⚠
- p.Cys190Ser Single submitter ⚠
- p.Gln222Arg Single submitter ⚠
- p.Glu105Gly Single submitter
- p.Glu228Gly Single submitter
- p.Glu275Gly Single submitter ⚠
- p.Glu279Gln Single submitter ⚠
- p.Glu308Asp Single submitter ⚠
- p.Glu311Gly Single submitter ⚠
- p.Glu311Lys Single submitter Jeune syndrome ⚠
- p.Glu48Asp Single submitter ⚠
- p.Glu63Gly Single submitter ⚠
- p.Glu92Gly Single submitter ⚠
- p.Gly187Ala Single submitter ⚠
- p.Gly243Arg Single submitter ⚠
- p.Gly80Ser Single submitter ⚠
- p.His217Tyr Single submitter ⚠
- p.Ile152Thr Single submitter ⚠
- p.Ile18Thr Single submitter ⚠
- p.Ile283Val Single submitter ⚠
- p.Ile295Val Single submitter ⚠
- p.Ile406Thr Single submitter ⚠
- p.Leu290Phe Single submitter ⚠
- p.Leu322Phe Single submitter ⚠
- p.Leu334Phe Single submitter ⚠
- p.Leu351Met Single submitter ⚠
- p.Leu356Phe Single submitter ⚠
- p.Lys127Thr Single submitter ⚠
- p.Lys54Glu Single submitter
- p.Met28Val Single submitter ⚠
- p.Met86Ile Single submitter ⚠
- p.Phe191Leu Single submitter ⚠
- p.Phe381Leu Single submitter ⚠
- p.Pro330Leu Single submitter ⚠
- p.Ser230Cys Single submitter ⚠
- p.Ser342Arg Single submitter
- p.Ser40Arg Single submitter ⚠
- p.Ser429Asn Single submitter ⚠
- p.Thr186Ile Single submitter ⚠
- p.Thr241Met Single submitter ⚠
- p.Thr333Asn Single submitter ⚠
- p.Thr359Met Single submitter ⚠
- p.Thr393_Ser394insVal Single submitter
- p.Thr66Ala Single submitter ⚠
- p.Thr97Ile Single submitter ⚠
- p.Tyr76Cys Single submitter ⚠
- p.Val116Ile Single submitter ⚠
- p.Val119Ala Single submitter ⚠
- p.Val306Ile Single submitter ⚠
- p.Val392Ala Single submitter
- p.Val410Ile Single submitter ⚠
- p.Val415Met Single submitter ⚠