Characteristics of pathogenic variants extracted from jMorp
| No. . | HGVS.c . | HGVS.p . | rs No. . | Allele frequency . | Allele count . | SIFT . | PolyPhen . | CADD . | PON-P2 . | InMeRF . | LOVD . | Selection criteria . |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | c.902A>G | p.Tyr301Cys | — | 0.0001 | 1 | deleterious(0) | probably_damaging(0.999) | 25.3 | Pathogenic | Pathogenic | — | PON+InM |
| 2 | c.1135T>G | p.Cys379Gly | rs763461692 | 0.0001 | 1 | deleterious(0) | probably_damaging(0.972) | 26.7 | Pathogenic | Pathogenic | — | PON+InM |
| 3 | c.1150T>C | p.Cys384Arg | rs762146804 | 0.0001 | 1 | deleterious(0) | benign(0.303) | 23.7 | Pathogenic | Pathogenic | — | PON+InM |
| 4 | c.1198G>C | p.Asp400His | — | 0.0001 | 1 | deleterious(0) | probably_damaging(0.999) | 26.9 | Pathogenic | Pathogenic | — | PON+InM |
| 5 | c.1312G>A | p.Ala438Thr | rs756620872 | 0.0001 | 1 | deleterious(0) | probably_damaging(0.995) | 25.1 | Pathogenic | Pathogenic | — | PON+InM |
| 6 | c.1788T>A | p.His596Gln | 0.0001 | 1 | deleterious(0) | probably_damaging(0.985) | 23.3 | Pathogenic | Pathogenic | — | PON+InM | |
| 7 | c.1862G>C | p.Cys621Ser | rs886049744 | 0.0001 | 1 | deleterious(0.02) | probably_damaging(0.985) | 28 | Pathogenic | Pathogenic | — | PON+InM |
| 8 | c.2137G>A | p.Gly713Ser | rs1418751948 | 0.0001 | 1 | deleterious(0) | probably_damaging(0.999) | 27.5 | Pathogenic | Pathogenic | — | PON+InM |
| 9 | c.2344C>T | p.Arg782Trp | rs61748471 | 0.0001 | 1 | deleterious(0) | possibly_damaging(0.828) | 22.8 | — | Pathogenic | Type 2N | database |
| 10 | c.2771_2775delGGGTC | p.Arg924HisfsTer10 | — | 0.0001 | 1 | — | — | — | — | — | — | variant type |
| 11 | c.2777_2778insTT | p.Ile927SerfsTer16 | — | 0.0001 | 1 | — | — | — | — | — | — | variant type |
| 12 | c.2819A>G | p.Glu940Gly | rs1268610851 | 0.0001 | 1 | deleterious(0.01) | probably_damaging(0.985) | 33 | — | — | — | CADD>20 |
| 13 | c.3433C>T | p.Arg1145Cys | — | 0.0001 | 1 | deleterious(0) | probably_damaging(1) | 27.8 | Pathogenic | Pathogenic | — | PON+InM |
| 14 | c.3797C>A | p.Pro1266Gln | rs61749370 | 0.001 | 12 | deleterious(0.01) | probably_damaging(0.994) | 23.5 | — | Pathogenic | Type 2B | database |
| 15 | c.3923G>A | p.Arg1308His | rs61749388 | 0.0001 | 1 | tolerated(1) | benign(0) | 17.38 | — | Pathogenic | Type 2A | database |
| 16 | c.3931C>T | p.Gln1311Ter | rs267607337 | 0.0005 | 8 | — | — | 42 | — | — | Type 3 | variant type, database, CADD>20 |
| 17 | c.4382C>T | p.Ala1461Val | rs61750089 | 0.0001 | 1 | tolerated(0.32) | possibly_damaging(0.596) | 21.7 | — | Pathogenic | Type 2B | database |
| 18 | c.5014G>A | p.Gly1672Arg | rs61750598 | 0.0023 | 38 | tolerated(0.55) | benign(0) | 10.01 | — | Pathogenic | Type 2A | database |
| 19 | c.5093delG | p.Gly1698AlafsTer13 | — | 0.0001 | 1 | — | — | — | — | — | — | variant type |
| 20 | c.5335C>T | p.Arg1779Ter | rs61750606 | 0.0002 | 3 | — | — | 41 | — | — | Type 1 | variant type, database, CADD>20 |
| 21 | c.5620+2T>G | — | rs758879278 | 0.0001 | 1 | — | — | 34 | — | — | — | variant type, CADD>20 |
| 22 | c.5827C>T | p.Arg1943Cys | — | 0.0002 | 3 | deleterious(0) | probably_damaging(0.926) | 32 | Pathogenic | — | — | CADD>20 |
| 23 | c.5840C>T | p.Pro1947Leu | rs1312789020 | 0.0001 | 1 | deleterious(0) | probably_damaging(0.997) | 32 | Pathogenic | — | — | CADD>20 |
| 24 | c.6311C>T | p.Thr2104Ile | rs61750616 | 0.0033 | 56 | deleterious(0) | probably_damaging(0.997) | 25.7 | Pathogenic | — | Type 1 | database |
| 25 | c.7080C>A | p.Cys2360Ter | — | 0.0001 | 1 | — | — | 35 | — | — | — | variant type, CADD>20 |
| 26 | c.7361C>A | p.Thr2454Asn | rs200486416 | 0.0001 | 1 | deleterious(0) | probably_damaging(0.979) | 25.6 | Pathogenic | Pathogenic | — | PON+InM |
| 27 | c.7400A>G | p.Gln2467Arg | — | 0.0001 | 1 | deleterious(0) | possibly_damaging(0.739) | 26.2 | Pathogenic | Pathogenic | — | PON+InM |
| 28 | c.7558C>T | p.Gln2520Ter | rs1448479214 | 0.0001 | 1 | — | — | 40 | — | — | Type 3 | variant type, database, CADD>20 |
| 29 | c.8113G>A | p.Gly2705Arg | rs7962217 | 0.0001 | 1 | deleterious(0) | probably_damaging(0.999) | 32 | Pathogenic | — | — | CADD>20 |
| No. . | HGVS.c . | HGVS.p . | rs No. . | Allele frequency . | Allele count . | SIFT . | PolyPhen . | CADD . | PON-P2 . | InMeRF . | LOVD . | Selection criteria . |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | c.902A>G | p.Tyr301Cys | — | 0.0001 | 1 | deleterious(0) | probably_damaging(0.999) | 25.3 | Pathogenic | Pathogenic | — | PON+InM |
| 2 | c.1135T>G | p.Cys379Gly | rs763461692 | 0.0001 | 1 | deleterious(0) | probably_damaging(0.972) | 26.7 | Pathogenic | Pathogenic | — | PON+InM |
| 3 | c.1150T>C | p.Cys384Arg | rs762146804 | 0.0001 | 1 | deleterious(0) | benign(0.303) | 23.7 | Pathogenic | Pathogenic | — | PON+InM |
| 4 | c.1198G>C | p.Asp400His | — | 0.0001 | 1 | deleterious(0) | probably_damaging(0.999) | 26.9 | Pathogenic | Pathogenic | — | PON+InM |
| 5 | c.1312G>A | p.Ala438Thr | rs756620872 | 0.0001 | 1 | deleterious(0) | probably_damaging(0.995) | 25.1 | Pathogenic | Pathogenic | — | PON+InM |
| 6 | c.1788T>A | p.His596Gln | 0.0001 | 1 | deleterious(0) | probably_damaging(0.985) | 23.3 | Pathogenic | Pathogenic | — | PON+InM | |
| 7 | c.1862G>C | p.Cys621Ser | rs886049744 | 0.0001 | 1 | deleterious(0.02) | probably_damaging(0.985) | 28 | Pathogenic | Pathogenic | — | PON+InM |
| 8 | c.2137G>A | p.Gly713Ser | rs1418751948 | 0.0001 | 1 | deleterious(0) | probably_damaging(0.999) | 27.5 | Pathogenic | Pathogenic | — | PON+InM |
| 9 | c.2344C>T | p.Arg782Trp | rs61748471 | 0.0001 | 1 | deleterious(0) | possibly_damaging(0.828) | 22.8 | — | Pathogenic | Type 2N | database |
| 10 | c.2771_2775delGGGTC | p.Arg924HisfsTer10 | — | 0.0001 | 1 | — | — | — | — | — | — | variant type |
| 11 | c.2777_2778insTT | p.Ile927SerfsTer16 | — | 0.0001 | 1 | — | — | — | — | — | — | variant type |
| 12 | c.2819A>G | p.Glu940Gly | rs1268610851 | 0.0001 | 1 | deleterious(0.01) | probably_damaging(0.985) | 33 | — | — | — | CADD>20 |
| 13 | c.3433C>T | p.Arg1145Cys | — | 0.0001 | 1 | deleterious(0) | probably_damaging(1) | 27.8 | Pathogenic | Pathogenic | — | PON+InM |
| 14 | c.3797C>A | p.Pro1266Gln | rs61749370 | 0.001 | 12 | deleterious(0.01) | probably_damaging(0.994) | 23.5 | — | Pathogenic | Type 2B | database |
| 15 | c.3923G>A | p.Arg1308His | rs61749388 | 0.0001 | 1 | tolerated(1) | benign(0) | 17.38 | — | Pathogenic | Type 2A | database |
| 16 | c.3931C>T | p.Gln1311Ter | rs267607337 | 0.0005 | 8 | — | — | 42 | — | — | Type 3 | variant type, database, CADD>20 |
| 17 | c.4382C>T | p.Ala1461Val | rs61750089 | 0.0001 | 1 | tolerated(0.32) | possibly_damaging(0.596) | 21.7 | — | Pathogenic | Type 2B | database |
| 18 | c.5014G>A | p.Gly1672Arg | rs61750598 | 0.0023 | 38 | tolerated(0.55) | benign(0) | 10.01 | — | Pathogenic | Type 2A | database |
| 19 | c.5093delG | p.Gly1698AlafsTer13 | — | 0.0001 | 1 | — | — | — | — | — | — | variant type |
| 20 | c.5335C>T | p.Arg1779Ter | rs61750606 | 0.0002 | 3 | — | — | 41 | — | — | Type 1 | variant type, database, CADD>20 |
| 21 | c.5620+2T>G | — | rs758879278 | 0.0001 | 1 | — | — | 34 | — | — | — | variant type, CADD>20 |
| 22 | c.5827C>T | p.Arg1943Cys | — | 0.0002 | 3 | deleterious(0) | probably_damaging(0.926) | 32 | Pathogenic | — | — | CADD>20 |
| 23 | c.5840C>T | p.Pro1947Leu | rs1312789020 | 0.0001 | 1 | deleterious(0) | probably_damaging(0.997) | 32 | Pathogenic | — | — | CADD>20 |
| 24 | c.6311C>T | p.Thr2104Ile | rs61750616 | 0.0033 | 56 | deleterious(0) | probably_damaging(0.997) | 25.7 | Pathogenic | — | Type 1 | database |
| 25 | c.7080C>A | p.Cys2360Ter | — | 0.0001 | 1 | — | — | 35 | — | — | — | variant type, CADD>20 |
| 26 | c.7361C>A | p.Thr2454Asn | rs200486416 | 0.0001 | 1 | deleterious(0) | probably_damaging(0.979) | 25.6 | Pathogenic | Pathogenic | — | PON+InM |
| 27 | c.7400A>G | p.Gln2467Arg | — | 0.0001 | 1 | deleterious(0) | possibly_damaging(0.739) | 26.2 | Pathogenic | Pathogenic | — | PON+InM |
| 28 | c.7558C>T | p.Gln2520Ter | rs1448479214 | 0.0001 | 1 | — | — | 40 | — | — | Type 3 | variant type, database, CADD>20 |
| 29 | c.8113G>A | p.Gly2705Arg | rs7962217 | 0.0001 | 1 | deleterious(0) | probably_damaging(0.999) | 32 | Pathogenic | — | — | CADD>20 |
The allele frequency expressed as "0.0001" is a rounded value to the fifth decimal place in the biobank; the actual value is "0.00006.”
CADD, Combined Annotation Dependent Depletion; HGVS, Human Genome Variation Society; HGVS.c, variant designations according to the HGVS nomenclature, based on coding DNA reference sequences; HGVS.p, variant designations according to HGVS nomenclature, based on protein reference sequence; InMeRF, Individual Meta Random Forest; PolyPhen, polymorphism phenotyping; PON-P2, Pathogenic-or-Not-Pipeline2; rs, reference SNP; SIFT, Sorting Intolerant from Tolerant.