General Structure Information
| PDB ID | 2dfd |
| HGNC Gene Label(s) | MDH2 |
| Structure Name | crystal structure of human malate dehydrogenase type 2 |
| Resolution | 1.9Å |
| Reference | AUTH E.UGOCHUKWU,N.SHAFQAT,A.ROJKOVA,M.SUNDSTROM,C.ARROWSMITH,AUTH 2 J.WEIGELT,A.EDWARDS,F.VON DELFT,U.OPPERMANNTITL CRYSTAL STRUCTURE OF HUMAN MALATE DEHYDROGENASE TYPE 2REF TO BE PUBLISHEDREFN |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 314 |
| Number Of SNVs | 111 |
| Number Of Permutations | 41697 |
| Optimal Distance Threshold | 9.0 |
| K Statistic | 0.038 |
| p-value | 0.72 |
COSMIC
| Number Of Residues | 314 |
| Number Of SNVs | 6 |
| Number Of Permutations | 1960 |
| Optimal Distance Threshold | 17.0 |
| K Statistic | 0.133 |
| p-value | 1.0 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 111 |
| Number Of COSMIC SNVs | 6 |
| Optimal Distance Threshold | 10.0 |
| K Statistic | -0.058 |
| p-value | 0.796 |
Pathogenic Proximity Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 7:75684166 | V>L | C:11 | (24.54, 163.99, 69.80) | |
| 7:75684169 | L>V | C:12 | (20.59, 164.94, 67.93) | |
| 7:75684178 | S>A | C:15 | (26.71, 159.74, 62.34) | |
| 7:75684190 | G>R | C:19 | (29.27, 164.18, 65.34) | |
| 7:75684196 | rs139725372 | P>T | C:21 | (34.06, 164.46, 65.83) |
| 7:75684208 | L>F | C:25 | (35.85, 165.85, 71.84) | |
| 7:75684229 | V>M | C:32 | (30.53, 163.53, 80.08) | |
| 7:75684256 | A>T | C:41 | (22.31, 156.48, 60.25) | |
| 7:75684257 | A>V | C:41 | (22.31, 156.48, 60.25) | |
| 7:75684260 | H>R | C:42 | (25.61, 154.70, 59.86) | |
| 7:75684272 | V>A | C:46 | (29.42, 155.48, 66.20) | |
| 7:75684277 | rs141539461 | A>T | C:48 | (30.77, 150.72, 69.49) |
| 7:75684292 | I>V | C:53 | (37.17, 155.27, 74.74) | |
| 7:75684295 | E>K | C:54 | (40.69, 154.59, 78.59) | |
| 7:75684307 | A>T | C:58 | (28.12, 155.98, 78.97) | |
| 7:75686739 | P>S | C:65 | (12.29, 157.80, 64.91) | |
| 7:75686756 | D>E | C:70 | (14.97, 156.06, 74.71) | |
| 7:75686765 | K>N | C:73 | (15.57, 160.42, 78.89) | |
| 7:75686766 | rs145477708 | G>C | C:74 | (17.75, 162.91, 81.09) |
| 7:75686788 | P>L | C:81 | (24.48, 168.50, 64.53) | |
| 7:75686799 | COSM3640626 | P>S | C:85 | (25.86, 170.22, 54.35) |
| 7:75686805 | K>E | C:87 | (28.06, 171.51, 47.85) | |
| 7:75687296 | R>Q | C:92 | (25.49, 179.77, 55.87) | |
| 7:75687314 | T>I | C:98 | (16.45, 170.88, 54.21) | |
| 7:75687317 | N>S | C:99 | (17.95, 171.89, 57.62) | |
| 7:75687322 | T>A | C:101 | (11.96, 169.84, 58.67) | |
| 7:75687323 | T>M | C:101 | (11.96, 169.84, 58.67) | |
| 7:75687335 | T>I | C:105 | (11.41, 167.22, 64.04) | |
| 7:75687343 | A>T | C:108 | (9.85, 168.47, 69.38) | |
| 7:75687362 | C>F | C:114 | (14.37, 167.08, 77.30) | |
| 7:75687365 | P>L | C:115 | (12.00, 169.93, 78.65) | |
| 7:75687371 | A>G | C:117 | (17.57, 170.94, 78.38) | |
| 7:75687374 | rs144979827 | M>T | C:118 | (20.76, 173.31, 78.18) |
| 7:75687382 | rs111879470 | V>I | C:121 | (21.27, 174.65, 67.43) |
| 7:75687388 | A>T | C:123 | (22.00, 173.63, 62.30) | |
| 7:75687395 | P>L | C:125 | (20.11, 178.38, 58.78) | |
| 7:75689701 | T>S | C:129 | (17.47, 177.22, 63.14) | |
| 7:75689703 | I>F | C:130 | (17.38, 179.42, 67.18) | |
| 7:75689709 | I>V | C:132 | (12.49, 176.93, 64.13) | |
| 7:75689713 | T>I | C:133 | (13.88, 175.93, 68.41) | |
| 7:75689721 | V>L | C:136 | (8.80, 174.23, 68.67) | |
| 7:75689728 | K>R | C:138 | (6.72, 179.39, 72.10) | |
| 7:75689733 | H>D | C:140 | (5.50, 171.60, 72.67) | |
| 7:75689739 | rs138541865 | V>M | C:142 | (8.37, 174.15, 77.33) |
| 7:75689740 | V>A | C:142 | (8.37, 174.15, 77.33) | |
| 7:75689746 | N>S | C:144 | (13.81, 178.67, 79.04) | |
| 7:75689748 | P>A | C:145 | (14.63, 181.87, 76.93) | |
| 7:75689749 | P>H | C:145 | (14.63, 181.87, 76.93) | |
| 7:75689755 | K>R | C:147 | (17.62, 176.30, 79.12) | |
| 7:75689763 | G>S | C:150 | (23.27, 179.31, 69.02) | |
| 7:75689766 | rs145207041 | V>M | C:151 | (26.43, 177.22, 68.25) |
| 7:75689770 | T>M | C:152 | (28.30, 181.21, 67.43) | |
| 7:75689778 | D>N | C:155 | (32.43, 182.65, 64.41) | |
| 7:75689784 | V>I | C:157 | (37.58, 179.83, 67.47) | |
| 7:75692838 | L>F | C:169 | (49.54, 186.42, 70.18) | |
| 7:75692842 | COSM1638365 | P>T | C:171 | (45.87, 181.24, 70.56) |
| 7:75692854 | N>D | C:175 | (39.40, 186.20, 74.29) | |
| 7:75692857 | V>I | C:176 | (37.32, 187.97, 69.94) | |
| 7:75692867 | I>T | C:179 | (28.26, 190.52, 67.78) | |
| 7:75692876 | H>R | C:182 | (26.76, 181.73, 61.57) | |
| 7:75692879 | A>D | C:183 | (25.85, 184.98, 58.12) | |
| 7:75692894 | I>N | C:188 | (29.70, 191.52, 64.05) | |
| 7:75692905 | S>A | C:192 | (37.30, 196.80, 70.14) | |
| 7:75693660 | T>A | C:195 | (41.23, 190.17, 75.34) | |
| 7:75693661 | T>N | C:195 | (41.23, 190.17, 75.34) | |
| 7:75693675 | F>L | C:200 | (44.94, 195.18, 64.01) | |
| 7:75693682 | Q>R | C:202 | (41.77, 201.03, 58.06) | |
| 7:75693684 | D>H | C:203 | (44.74, 197.73, 55.92) | |
| 7:75693697 | COSM3950805 | A>V | C:207 | (40.74, 191.97, 56.19) |
| 7:75693703 | T>I | C:209 | (36.55, 191.60, 59.58) | |
| 7:75693708 | rs139870141 | R>G | C:211 | (40.43, 185.06, 57.30) |
| 7:75693709 | R>Q | C:211 | (40.43, 185.06, 57.30) | |
| 7:75693718 | E>A | C:214 | (33.57, 185.04, 54.14) | |
| 7:75693723 | G>S | C:216 | (33.24, 179.05, 55.80) | |
| 7:75693727 | T>M | C:217 | (32.67, 180.18, 52.39) | |
| 7:75693732 | rs147530406 | V>M | C:219 | (36.24, 175.57, 54.55) |
| 7:75693739 | K>R | C:221 | (36.80, 177.23, 47.87) | |
| 7:75693748 | A>V | C:224 | (35.45, 170.46, 46.89) | |
| 7:75693750 | rs139907444 | G>R | C:225 | (32.18, 168.87, 48.08) |
| 7:75694131 | L>F | C:231 | (37.46, 168.60, 62.57) | |
| 7:75694137 | M>V | C:233 | (32.00, 172.87, 64.99) | |
| 7:75694149 | G>S | C:237 | (31.10, 172.58, 70.66) | |
| 7:75694152 | rs147655350 | A>T | C:238 | (32.86, 171.13, 72.94) |
| 7:75694155 | R>C | C:239 | (34.67, 176.87, 73.79) | |
| 7:75694156 | R>H | C:239 | (34.67, 176.87, 73.79) | |
| 7:75694161 | V>I | C:241 | (29.08, 171.70, 76.04) | |
| 7:75694171 | L>R | C:244 | (26.76, 175.07, 79.25) | |
| 7:75694182 | COSM381608 | M>V | C:248 | (25.18, 173.35, 84.84) |
| 7:75694186 | N>S | C:249 | (28.88, 172.10, 87.78) | |
| 7:75694194 | E>Q | C:252 | (32.07, 181.89, 89.68) | |
| 7:75694197 | G>S | C:253 | (32.78, 183.45, 84.77) | |
| 7:75694212 | S>A | C:258 | (25.12, 182.70, 71.67) | |
| 7:75694218 | COSM1091807 | V>I | C:260 | (20.19, 184.20, 72.08) |
| 7:75694225 | S>L | C:262 | (17.57, 189.48, 72.28) | |
| 7:75694234 | COSM1091808 | T>M | C:265 | (18.78, 194.76, 69.03) |
| 7:75694240 | rs148746442 | C>Y | C:267 | (16.75, 191.82, 66.74) |
| 7:75694245 | Y>H | C:269 | (15.63, 185.46, 68.26) | |
| 7:75694252 | rs142336603 | S>C | C:271 | (25.05, 187.19, 69.40) |
| 7:75694269 | G>R | C:277 | (24.77, 179.20, 84.72) | |
| 7:75694270 | G>A | C:277 | (24.77, 179.20, 84.72) | |
| 7:75695601 | K>M | C:279 | (19.03, 178.44, 86.35) | |
| 7:75695609 | E>K | C:282 | (23.03, 184.26, 85.35) | |
| 7:75695613 | rs10256 | K>R | C:283 | (23.87, 189.20, 82.88) |
| 7:75695619 | L>R | C:285 | (27.15, 190.70, 79.22) | |
| 7:75695624 | I>V | C:287 | (26.59, 195.24, 72.18) | |
| 7:75695627 | G>S | C:288 | (28.80, 197.47, 74.35) | |
| 7:75695631 | COSM71604 | K>R | C:289 | (31.82, 199.85, 73.76) |
| 7:75695640 | S>C | C:292 | (32.16, 203.56, 64.32) | |
| 7:75695643 | F>S | C:293 | (34.32, 199.08, 61.29) | |
| 7:75695646 | E>A | C:294 | (32.44, 197.62, 65.63) | |
| 7:75695652 | K>M | C:296 | (28.14, 201.47, 59.88) | |
| 7:75695657 | I>V | C:298 | (25.34, 196.48, 64.34) | |
| 7:75695661 | COSM240626 | S>L | C:299 | (23.08, 198.79, 60.91) |
| 7:75695675 | E>K | C:304 | (20.48, 189.41, 56.91) | |
| 7:75695691 | I>N | C:309 | (14.20, 186.02, 62.77) | |
| 7:75695693 | rs144919730 | K>Q | C:310 | (9.50, 186.66, 59.11) |
| 7:75695694 | K>R | C:310 | (9.50, 186.66, 59.11) | |
| 7:75695706 | D>G | C:314 | (6.71, 182.61, 58.96) | |
| 7:75695711 | rs140381447 | V>M | C:316 | (6.56, 177.14, 62.88) |
| 7:75695716 | K>N | C:317 | (3.13, 179.29, 61.34) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 7:75687331 | COSM1623100 | A>S | C:104 | (11.36, 170.90, 64.05) |
| 7:75692906 | COSM747086 | S>C | C:192 | (37.30, 196.80, 70.14) |
| 7:75693664 | COSM107757 | P>L | C:196 | (44.78, 191.05, 74.17) |
| 7:75694218 | COSM1091807 | V>I | C:260 | (20.19, 184.20, 72.08) |
| 7:75694234 | COSM1091808 | T>M | C:265 | (18.78, 194.76, 69.03) |
| 7:75695598 | COSM3734257 | K>R | C:278 | (23.33, 176.83, 87.69) |