Skip to main content
. 2021 Mar 12;13(6):1259. doi: 10.3390/cancers13061259

Table 2.

Somatic bi- and monoallelic variants in core and associated MMR genes.

Sample ID Gene Name HGVS.c HGVS.p Variant Impact gnomAD ClinVar COSMIC PolyPhen2 SIFT CADD Tumor AF Average Sample AF LOH AF Increase over Average (%) LOH
Biallelic Somatic Variants
LLS02 MSH3 c.423C > A p.Cys141 * stop_gained not present not present not present - - 38 0.60 0.35 73 yes
LLS09 MSH3 c.1148delA p.Lys383fs frameshift_variant 1.64399 × 10−5 Pathogenic COSM1438888 - - - 0.46 0.33 40 yes
LLS10 MSH3 c.1148delA p.Lys383fs frameshift_variant 1.64399 × 10−5 Pathogenic COSM1438888 - - - 0.61 0.35 75 yes
LLS10 POLD1 c.583C > T p.Arg195 * stop_gained 0.000647 Conflicting not present - - 37 0.36 0.35 5 no
LLS10 POLD1 c.2959delG p.Asp987fs frameshift_variant 0.000057209 not present COSM3686158 - - - 0.40 0.35 15 no
LLS17 MLH1 c.129dupA p.Ser44fs frameshift_variant not present Pathogenic not present - - - 0.22 0.25 −14 no
LLS17 MLH1 c.1831delA p.Ile611fs frameshift_variant not present not present not present - - - 0.33 0.25 31 no
LLS18 MSH2 c.2251G > T p.Gly751 * stop_gained not present not present not present - - 48 0.15 0.17 −11 no
LLS18 MSH2 c.2634+1G > A - splice_variant not present Likely_pathogenic not present - - 27.6 0.19 0.17 14 no
LLS21 MLH1 c.199G > A p.Gly67Arg missense_variant not present Pathogenic COSM1422567 D D 34 0.13 0.18 −25 no
LLS21 MLH1 c.602delT p.Val201fs frameshift_variant not present not present not present - - - 0.24 0.18 36 no
LLS5159 POLD1 c.1562G > A p.Arg521Gln missense_variant 0.000126296 VUS not present P D 31 0.22 022 4 no
LLS5159 POLD1 c.3047G > A p.Arg1016His missense_variant not present VUS COSM7587416 P D 29.6 0.27 0.22 25 no
LLS9045 MLH3 c.3694C > T p.Arg1232Cys missense_variant 3.24934 × 10−5 VUS not present D D 31 0.28 0.28 4 no
LLS9045 MLH3 c.1924T > C p.Phe642Leu missense_variant not present not present not present B D 20.1 0.46 0.28 68 yes
LLS9045 MLH1 c.588delA p.Lys196fs frameshift_variant 4.06276 × 10−6 Pathogenic not present - - - 0.22 0.28 −21 no
LLS9045 MLH1 c.1489delC p.Arg497fs frameshift_variant 4.06078 × 10−6 not present COSM1422596 - - - 0.21 0.28 −23 no
LLS9049 POLD1 c.2959delG p.Asp987fs frameshift_variant 0.000057209 not present COSM3686158 - - - 0.31 0.19 57 yes
Monoallelic Somatic Variants
LLS09 MSH6 c.3552G > A p.Met1184Ile missense_variant 4.06835 × 10−6 not present not present B T 28 0.30 0.33 −10 no
LLS10 MSH6 c.2875C > T p.Arg959Cys missense_variant 1.22491 × 10−5 VUS not present P D 27.2 0.34 0.35 −1 no
LLS10 POLE c.2091delC p.Leu698fs frameshift_variant 8.20836 × 10−6 VUS COSM4612998 - - - 0.27 0.35 −21 no
LLS18 MSH6 c.3261dupC p.Phe1088fs frameshift_variant 0.00003449 Pathogenic COSM13394 - - - 0.13 0.17 −23 no
LLS19 MSH2 c.1225C > T p.Gln409 * stop_gained not present Pathogenic COSM7508782 - - 41 0.16 0.15 7 no
LLS19 MSH6 c.1993G > A p.Glu665Lys missense_variant 4.06792 × 10−6 not present not present P T 24.9 0.12 0.15 −18 no
LLS21 MSH3 c.3356T > C p.Leu1119Pro missense_variant not present not present not prensent D D 27.3 0.14 0.18 −20 no
LLS21 PMS2 c.1239delA p.Asp414fs frameshift_variant not present not present COSM150905 - - - 0.20 0.18 12 no
LLS21 POLE c.1060A > G p.Thr354Ala missense_variant not present not present not present B T 22.5 0.20 0.18 11 no
LLS9045 MUTYH c.724C > T p.Arg242Cys missense_variant 5.29614 × 10−5 Pathogenic COSM6954579 D D 29.5 0.36 0.28 32 no
LLS9045 POLD1 c.735G > T p.Glu245Asp missense_variant not present not present not present D T 22.9 0.27 0.28 −2 no
LLS9049 MUTYH c.544C > T p.Arg182Trp missense_variant 1.21817 × 10−5 not present COSM6922477 D T 23.3 0.13 0.19 −32 no
LLS9049 MSH3 c.433G > T p.Ala145Ser missense_variant not present VUS not present P T 17.64 0.15 0.19 −23 no
LLS9049 POLE c.3176G > A p.Arg1059His missense_variant 1.21838 × 10−5 not present COSM6965827 D D 35 0.20 0.19 2 no

Rows in bold are showing when LOH is associated. GnomAD: allele frequency from gnomAD database. PolyPhen2: B: benign; P: probably pathogenic; D: deleterious; SIFT: T: tolerable; D: deleterious. Tumor AF: alternative allele frequency. Average AF: average of all exome variants over 0.1 of AF. LOH loss of heterozygosity. CADD: Phred score version 1.6. VUS: variant of uncertain significance. HGVS.c: coding variant. HGVS.p: protein level variant. * stop gained codon.