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Table 2 SORL1 variations. All SORL1 variations found to be likely pathogenic or of uncertain significance according to ACMG criteria [25] generated using three independent study cohorts

From: Identification and description of three families with familial Alzheimer disease that segregate variants in the SORL1 gene

Domain Transcript Variant Coding effect Protein change Predictions SIFT/MutTas Prediction Splice-site effect MaxEnt/NNSPLICE/HSF dbSNP ID ExAC European
Case/Control EU EOD Swedes
Segregates with disease Family number Classification ACMG Study cohort
11:121340732 VPS10p c.302C > T (NM_003105.5) Missense p.Ser101Phe Deleterious/Disease causing −1.3% 0.26/0 Unknown FH Uncertain sign. case-control
11:121383766 VPS10p c.994C > T (NM_003105.5) Missense p.Arg332Trp Deleterious/Disease causing None rs772110877 0.01049 0.26/0 Unknown FH Uncertain sign. case-control
11:121391400 VPS10p c.1246C > T (NM_003105.5) Nonsense p.Arg416* not applicable −0.1% rs144585461 0.26/0 Unknown FH a Likely path. case-control
11:121437647 EGF c.3050-2A < G (NM_003105.5) Deletion p.Gly1017-Glu1074del not applicable −100% 0/0 yes
Likely path. Targeted re-seq.
11:121458821 LDLR class A c.3907C > T (NM_003105.5) Missense p.Arg1303Cys Deleterious/Disease causing None rs781023219 0.005995 0/0 yes
Likely path. WES-family
11:121460051 LDLR class A c.4030 T > C (NM_003105.5) Missense p.Cys1344Arg Deleterious/Disease causing None 0.26/0 Possible FH b Uncertain sign. case-control
11:121478841 Fibronectin type III c.5195G > C (NM_003105.5) Missense p.Gly1732Ala Deleterious/Disease causing None rs777194720 0.007499 0.26/0 yes
Uncertain sign. case-control
  1. FH Family history
  2. a Originates from Chile
  3. b Originates from Finland