Table II.
Characterization of genetic variants identified in the present study and their pathogenicity analysis.
| A, Novela LDLR variants, reported in this study | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Patient ID | Genetic variant | Number of patients | Variant ID in dbSNP or alternative database | Genomic position (GCRh37/hg19) | Pathogenicity analysisb MAF in GnomAD | Functional domain | Pathogenicityc | SIFT | Mutation taster | Poly Phen2 | (Refs.) |
| 1 | Missense Exon 4 c.325T>G p.(Cys109Gly) | 1 | 869387 in ClinVar | Chr19: 11215907 | - | Ligand-binding | Likely pathogenic (PS1 PM1 PM2 PM5 PP3) | D | D | D | - |
| 2 | Missense Exon 4 c.401G>C p.(Cys134Ser) | 1 | 869388 in ClinVar | Chr19: 11215983 | - | Ligand-binding | Likely pathogenic (PS1 PM1 PM2 PM5 PP3) | D | D | D | - |
| 3 | Frameshift Exon 4 c.433_434dupG p.(Val145Glyfs*35) | 1 | 870329 in ClinVar | Chr19: 11216013 | - | Ligand-binding | Pathogenic (PVS1 PM2 PP3) | D | D | -- | - |
| 4 | Missense Exon 4 c.616A>C p.(Ser206Arg) | 1 | 869389 in ClinVar | Chr19: 11216198 | - | Ligand-binding | Uncertain value (PM2 PP3) | D | D | D | - |
| 5 | c.940+1_c.940+ 4 delGTGA (g.18154_18157 delGTGA) | 4 | 869390 in ClinVar | Chr19: 11218191-11218194 | - | Splice donor site, intron 6 | Pathogenic (PVS1 PM1 PM2 PP3) | -- | D | -- | - |
| 6 | Missense Exon 8 c.1186G>C p.(Gly396Arg) | 1 | 870321 in ClinVar | Chr19: 11222315 | - | EGF precursor homology B repeat | Pathogenic (PVS1 PM1 PM2 PM5 PP3) | D | D | D | - |
| 7 | Frameshift Exon 11 c.1684_1691del TGGCCCAA p.(Pro563Hisfs*14) | 1 | 869391 in ClinVar | Chr19: 11226866-11226875 | - | EGF spacer | Pathogenic (PVS1 PM1 PM2 PP3) | D | D | -- | - |
| B, Genetic variants in LDLR | |||||||||||
| 8 | Missense Exon 2 c.100T>G p.(Cys34Gly) | 1 | rs879254405 | Chr19: 11210931 | - | Ligand-binding | Pathogenic/ Likely pathogenic | D | D | D | (12,59) |
| 9 | Frameshift Exon 4 c.316_328delCCC AAGACGTGCT p.(Lys107Argfs*95) | 1 | LDLR_001035 in LOVD database | Chr19: 11215901-11215915 | - | Ligand-binding | Pathogenic | D | D | -- | (39) |
| 10 | Missense Exon 4 c.552T>G p.(Cys184Trp) | 1 | LDLR_000858 in LOVD database | Chr19: 11216134 | - | Ligand-binding | Likely pathogenic | D | D | D | (40) |
| 11 | Missense Exon 5 c.798T>A p.(Asp266Glu)d | 1 | rs139043155 | Chr19: 11217344 | 0.000032 | Ligand-binding | Pathogenic/ Likely pathogenic | D | D | - | (50,55-58,65) |
| 12 | Missense Exon 6 c.887G>A p.(Cys296Tyr) | 1 | rs879254707 | Chr19: 11218137 | - | Ligand-binding | Likely pathogenic | D | D | D | (51,62) |
| 13 | Nonsense Exon 6 c.888C>A p.(Cys296*) | 1 | rs879254708 | Chr19: 11218138 | - | Ligand-binding | Pathogenic | D | D | -- | (52) |
| 14 | Missense Exon 6 c.938 G>A p.(Cys313Tyr) | 1 | rs875989910 | Chr19: 11218188 | - | Ligand-binding | Pathogenic/ Likely pathogenic | D | D | D | (63) |
| 15 | Missense Exon 7 c.986G>A p.(Cys329Tyr)d | 2 | rs761954844 | Chr19: 11221373 | 0.000016 | EGF precursor homology repeat A | Likely pathogenic | D | D | D | (12,39,50,65) |
| 16 | Nonsense Exon 7 c.1048C>T p.(Arg350*) | 1 | rs769737896 | Chr19: 11221435 | - | EGF precursor homology repeat A | Pathogenic | D | D | -- | (32,51,53) |
| 17 | c.1186+1G>T | 1 | rs730880131 | Chr19: 11222316 | - | Splice donor site‡, intron 8 | Pathogenic/ Likely pathogenic | -- | D | -- | - |
| 18 | Missense Exon 9 c.1202T>A p.(Leu401His) | 3 | rs121908038 | Chr19: 11223969 | - | EGF spacer | Likely pathogenic | D | D | D | (12) |
| 19 | Missense Exon 9 c.1277 T>C p.(Leu426Pro) | 1 | rs879254851 | Chr19: 11224044 | - | EGF spacer | Pathogenic/ conflicting- interpretations-of- pathogenicity | D | D | B | (66) |
| 20 | Frameshift Exon 10 c.1478_1479delCT p.(Ser493Cysfs*42) | 1 | rs869025453 | Chr19: 11113652-11113655 | 0.00003 | EGF spacer | Pathogenic/ Likely pathogenic | -- | D | -- | (39,40) |
| 21 | Missense Exon 12 c.1730G>C p.(Trp577Ser) | 1 | rs138947766 | Chr19: 11227559 | 0.000008 | EGF spacer | Pathogenic/ Likely pathogenic | D | D | D | (39) |
| 22 | Missense Exon 12 c.1775G>A p.(Gly592Glu) | 6 | rs137929307 | Chr19: 11227604 | 0.000044 | EGF spacer | Pathogenic/ Likely pathogenic | D | D | D | (40,50,65) |
| 23 | Nonsense Exon 15 c.2230C>T p.(Arg744*) | 1 | rs200793488 | Chr19: 11233939 | 0.000004 | O-linked sugars | Pathogenic | D | D | - | (62) |
| C, Genetic variants in APOB | |||||||||||
| 24 | Missense Exon 26 c.9175C>T p.(Arg3059Cys)d | 1 | rs146377316 | Chr2: 21230565 | 0.000008 | LDLR binding | Unknown significance | B | B | B | (35,42) |
| 25 | Missense Exon 26 c.10580G>A p.(Arg3527Gln)d | 1 | rs5742904 | Chr2: 21229160 | 0.000275 | LDLR binding | Pathogenic | B | D | D | (41) |
| 26 | Missense Exon 26 c.10580G>T p.(Arg3527Leu) | 1 | rs5742904 | Chr2: 21229160 | - | LDLR binding | Pathogenic | D | D | D | (39,40,41) |
| 27 | In-frame deletion Exon 29 c.13480_ 13482delCAG p.(Gln4494del)d | 2 | rs562574661 | Chr2: 21001940-21001945 | 0.000384 | - | Likely pathogenic/ conflicting- interpretations-of- pathogenicity | - | B | - | (41) |
| D, Genetic variants in ABCG5/8 | |||||||||||
| 28 | Nonsense ABCG5 Exon 10 c.1336C>T p.(Arg446*) | 1 | rs199689137 | Chr2: 44050063 | 0.00018 | Cytoplasmic | Pathogenic | D | D | - | (43,45,46) |
| 29 | Missense ABCG8 Exon 7 c.1083G>A p.(Trp361*) | 1 | rs137852987 | Chr2: 44099233 | 0.00102 | Cytoplasmic | Pathogenic | D | D | - | (47,67) |
| 30 | Missense ABCG8 Exon 11 c.1629G>T p.(Arg543Ser)d | 1 | rs201690654 | Chr2, 44102425 | 0.000215 | Transmembrane | Unknown significance | D | D | D | (48,49) |
| E, Genetic variant in LIPA | |||||||||||
| 31 | c.894G>A p. (Q298=) | 1 | rs116928232 | Chr10: 89222511 | 0.00083 | Exon skipping mutation | Pathogenic | -- | D | -- | (38) |
| F, Genetic variant in PCSK9 | |||||||||||
| 32 | Missense Exon 9 c.1486C>T p.(Arg496Trp) | 1 | rs374603772 | Chr1, 55524303 | 0.000044 | LDLR-binding | Unknown significance/ conflicting- interpretations-of- pathogenicity | D | D | D | (68,69) |
aThe frequency of the identified variants was additionally assessed following in-house exome databases. Novel variants were not found in the Russian 870 exomes and the Northwest Russia 694 exomes databases.
bThe prediction of the pathogenicity was performed using SIFT, PolyPhen-2 and MutationTaster tools if suitable. For two intronic variants, analysis with Human Splicing Finder was performed: These variants alter canonical splice donor sites in introns 6 and 8 of the LDLR gene, respectively.
cPathogenicity prediction for novel variants was performed according to American College of Medical Genetics and Genomics-based classification, for already characterized variants-classification according to ClinVar database.
dThese variants were functionally characterized by ex vivo or in vitro studies. In the case of LDLR <30% of normal receptor activity was seen; in the case of APOB reduction in the binding and uptake of LDL was observed; in the case of ABCG8 the amount of mature protein was decreased. B, benign; D, damaging/disease causing.