General Structure Information
| PDB ID | 2vdy |
| HGNC Gene Label(s) | SERPINA6 |
| Structure Name | crystal structure of the reactive loop cleaved corticosteroid binding globulin complexed with cortisol |
| Resolution | 2.3Å |
| Reference | AUTH A.ZHOU,Z.WEI,P.L.STANLEY,R.J.READ,P.E.STEIN,R.W.CARRELLTITL THE S-TO-R TRANSITION OF CORTICOSTEROID-BINDING GLOBULINTITL 2 AND THE MECHANISM OF HORMONE RELEASE.REF J.MOL.BIOL. V. 380 244 2008REFN ISSN 0022-2836PMID 18513745DOI 10.1016/J.JMB.2008.05.012 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 361 |
| Number Of SNVs | 102 |
| Number Of Permutations | 18262 |
| Optimal Distance Threshold | 7.0 |
| K Statistic | 0.016 |
| p-value | 0.144 |
COSMIC
| Number Of Residues | 361 |
| Number Of SNVs | 10 |
| Number Of Permutations | 2896 |
| Optimal Distance Threshold | 5.0 |
| K Statistic | 0.022 |
| p-value | 0.445 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 102 |
| Number Of COSMIC SNVs | 7 |
| Optimal Distance Threshold | 11.0 |
| K Statistic | -0.063 |
| p-value | 0.537 |
Pathogenic Proximity Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 14:94780873 | G>V | A:16 | (-13.65, 2.68, -26.95) | |
| 14:94780874 | G>S | A:16 | (-13.65, 2.68, -26.95) | |
| 14:94780871 | L>V | A:17 | (-13.24, 7.17, -27.61) | |
| 14:94780855 | rs537835110 | V>A | A:22 | (-16.52, 5.52, -36.00) |
| 14:94780856 | V>I | A:22 | (-16.52, 5.52, -36.00) | |
| 14:94780814 | S>C | A:36 | (-32.10, 14.59, -46.17) | |
| 14:94780803 | K>N | A:39 | (-29.57, 18.33, -48.04) | |
| 14:94780771 | rs199720892 | M>T | A:50 | (-15.83, 17.33, -28.57) |
| 14:94780768 | rs146744332 | A>V | A:51 | (-20.18, 18.77, -27.96) |
| 14:94780732 | T>I | A:63 | (-30.54, 12.74, -19.61) | |
| 14:94780729 | rs199541890 COSM1608093 COSM1608092 |
R>Q | A:64 | (-25.30, 10.93, -16.87) |
| 14:94780730 | rs199699199 COSM1563031 COSM1563032 |
R>W | A:64 | (-25.30, 10.93, -16.87) |
| 14:94780682 | E>K | A:80 | (-17.90, 10.50, -17.40) | |
| 14:94780678 | T>S | A:81 | (-12.97, 9.98, -16.49) | |
| 14:94780653 | H>Q | A:89 | (-5.40, 12.72, -26.88) | |
| 14:94780655 | rs187253929 | H>Y | A:89 | (-5.40, 12.72, -26.88) |
| 14:94780642 | rs113418909 | L>H | A:93 | (-3.29, 15.72, -31.12) |
| 14:94780643 | L>I | A:93 | (-3.29, 15.72, -31.12) | |
| 14:94780628 | rs377478491 | D>H | A:98 | (2.46, 23.87, -39.94) |
| 14:94780615 | rs202107375 | E>G | A:102 | (-3.88, 25.33, -40.37) |
| 14:94780605 | M>I | A:105 | (-11.00, 21.43, -32.27) | |
| 14:94780606 | M>T | A:105 | (-11.00, 21.43, -32.27) | |
| 14:94780607 | M>V | A:105 | (-11.00, 21.43, -32.27) | |
| 14:94780597 | A>V | A:108 | (-17.67, 27.51, -25.92) | |
| 14:94780578 | rs576835982 | S>R | A:114 | (-28.82, 35.08, -14.68) |
| 14:94780569 | L>F | A:117 | (-21.52, 27.62, -14.20) | |
| 14:94780565 | E>K | A:119 | (-16.30, 24.83, -9.19) | |
| 14:94780561 | S>L | A:120 | (-17.57, 20.89, -11.06) | |
| 14:94780528 | rs141500229 | S>L | A:131 | (-14.02, 26.06, -22.41) |
| 14:94780529 | rs374185317 | S>T | A:131 | (-14.02, 26.06, -22.41) |
| 14:94780510 | N>S | A:137 | (-27.70, 40.29, -22.53) | |
| 14:94780486 | COSM144405 | S>N | A:145 | (-26.34, 36.70, -32.34) |
| 14:94780479 | Q>H | A:147 | (-21.15, 37.68, -28.85) | |
| 14:94780478 | I>F | A:148 | (-22.18, 33.74, -30.79) | |
| 14:94780469 | Y>N | A:151 | (-15.92, 32.81, -30.69) | |
| 14:94780461 | K>N | A:153 | (-17.22, 34.50, -38.40) | |
| 14:94780447 | G>E | A:158 | (-14.25, 32.60, -42.08) | |
| 14:94780441 | I>T | A:160 | (-18.33, 29.02, -40.24) | |
| 14:94780436 | rs182173676 | D>N | A:162 | (-24.12, 33.90, -40.57) |
| 14:94780411 | P>Q | A:170 | (-34.07, 33.45, -27.90) | |
| 14:94780400 | COSM2151408 COSM2151407 |
V>I | A:174 | (-25.00, 28.91, -26.11) |
| 14:94780387 | Y>C | A:178 | (-13.90, 25.97, -32.70) | |
| 14:94780379 | F>L | A:181 | (-8.56, 20.28, -42.43) | |
| 14:94776340 | T>K | A:184 | (-1.76, 19.78, -48.62) | |
| 14:94776332 | rs142314764 | Q>E | A:187 | (-0.87, 12.37, -54.84) |
| 14:94776328 | COSM335811 | P>R | A:188 | (-0.81, 17.23, -56.38) |
| 14:94776319 | L>R | A:191 | (-3.32, 23.51, -62.23) | |
| 14:94776307 | rs144992509 | R>T | A:195 | (-9.97, 21.28, -69.01) |
| 14:94776301 | E>G | A:197 | (-16.51, 17.58, -66.85) | |
| 14:94776298 | N>I | A:198 | (-21.21, 17.52, -67.56) | |
| 14:94776289 | V>A | A:201 | (-27.50, 15.91, -60.05) | |
| 14:94776287 | COSM1371786 COSM1371787 |
D>N | A:202 | (-30.84, 14.43, -60.90) |
| 14:94776284 | rs370762935 COSM1707814 COSM1707815 |
E>K | A:203 | (-32.22, 11.01, -64.77) |
| 14:94776263 | P>S | A:210 | (-14.74, 22.78, -62.07) | |
| 14:94776259 | M>T | A:211 | (-13.42, 17.95, -63.34) | |
| 14:94776260 | M>V | A:211 | (-13.42, 17.95, -63.34) | |
| 14:94776247 | COSM1637222 COSM1637223 |
S>L | A:215 | (-2.04, 10.43, -64.01) |
| 14:94776244 | S>N | A:216 | (-1.29, 9.03, -60.51) | |
| 14:94776242 | T>A | A:217 | (0.34, 5.67, -58.41) | |
| 14:94776235 | S>N | A:219 | (-4.83, 3.72, -53.61) | |
| 14:94776230 | L>F | A:221 | (-10.90, -1.20, -54.33) | |
| 14:94776221 | rs2228541 | S>A | A:224 | (-16.68, -7.40, -55.10) |
| 14:94776212 | P>T | A:227 | (-22.12, -1.41, -55.71) | |
| 14:94776187 | Y>C | A:235 | (-4.87, 15.32, -46.79) | |
| 14:94776185 | COSM4053225 COSM4053226 |
V>M | A:236 | (0.87, 16.91, -45.58) |
| 14:94776181 | G>V | A:237 | (0.53, 14.11, -42.61) | |
| 14:94776160 | I>T | A:244 | (-16.63, 6.28, -52.20) | |
| 14:94776151 | D>G | A:247 | (-22.36, 1.72, -59.31) | |
| 14:94776141 | K>N | A:250 | (-26.81, 1.26, -56.64) | |
| 14:94776128 | rs201288144 | I>F | A:255 | (-24.70, 4.90, -47.45) |
| 14:94776112 | rs267604111 COSM26307 COSM267404 COSM1265285 |
R>Q | A:260 | (-15.85, -0.70, -37.00) |
| 14:94776108 | rs201033879 | D>E | A:261 | (-16.16, -4.36, -40.66) |
| 14:94776110 | D>N | A:261 | (-16.16, -4.36, -40.66) | |
| 14:94776106 | COSM1470746 COSM1470747 |
T>M | A:262 | (-16.51, -1.66, -44.87) |
| 14:94776096 | R>S | A:265 | (-13.69, -4.90, -47.20) | |
| 14:94776089 | rs202078426 COSM4053223 COSM4053224 |
A>T | A:268 | (-6.98, -4.27, -47.29) |
| 14:94776086 | G>S | A:269 | (-7.76, -3.69, -50.79) | |
| 14:94772542 | Y>H | A:278 | (-11.13, 12.60, -64.33) | |
| 14:94772539 | rs374191911 | I>V | A:279 | (-11.96, 15.15, -58.20) |
| 14:94772535 | rs546678080 | P>R | A:280 | (-14.99, 17.70, -58.45) |
| 14:94772520 | S>F | A:285 | (-22.79, 24.34, -47.62) | |
| 14:94772503 | G>R | A:291 | (-33.10, 16.56, -33.72) | |
| 14:94772483 | M>I | A:297 | (-29.43, 8.03, -32.70) | |
| 14:94772476 | A>S | A:300 | (-34.79, 12.71, -26.33) | |
| 14:94772472 | D>G | A:301 | (-34.60, 12.88, -22.42) | |
| 14:94772473 | rs200758120 | D>Y | A:301 | (-34.60, 12.88, -22.42) |
| 14:94772457 | Q>R | A:306 | (-39.21, 15.82, -18.35) | |
| 14:94772451 | N>S | A:308 | (-31.27, 15.98, -15.56) | |
| 14:94772447 | F>L | A:309 | (-29.34, 19.90, -18.53) | |
| 14:94772442 | R>H | A:311 | (-23.38, 17.44, -13.67) | |
| 14:94772440 | I>V | A:312 | (-24.97, 23.07, -16.07) | |
| 14:94772427 | A>D | A:316 | (-31.86, 26.76, -13.58) | |
| 14:94772428 | A>T | A:316 | (-31.86, 26.76, -13.58) | |
| 14:94772413 | S>P | A:321 | (-34.06, 24.35, -27.73) | |
| 14:94770936 | rs537163230 | V>A | A:324 | (-27.55, 23.47, -35.19) |
| 14:94770933 | H>R | A:325 | (-23.34, 20.90, -37.82) | |
| 14:94770916 | L>F | A:331 | (-12.22, 20.26, -52.96) | |
| 14:94770912 | rs147297630 | N>S | A:332 | (-8.11, 22.78, -54.38) |
| 14:94770913 | N>H | A:332 | (-8.11, 22.78, -54.38) | |
| 14:94770906 | E>A | A:334 | (-3.50, 23.13, -54.52) | |
| 14:94770854 | rs528742561 | K>N | A:351 | (-3.99, 1.83, -69.91) |
| 14:94770855 | K>T | A:351 | (-3.99, 1.83, -69.91) | |
| 14:94770840 | rs149012523 | R>H | A:356 | (-14.89, 10.60, -65.11) |
| 14:94770837 | F>C | A:357 | (-15.59, 10.95, -58.54) | |
| 14:94770835 | N>H | A:358 | (-19.57, 12.51, -63.25) | |
| 14:94770829 | P>T | A:360 | (-23.67, 11.46, -56.94) | |
| 14:94770820 | I>V | A:363 | (-16.24, 12.59, -49.01) | |
| 14:94770817 | M>V | A:364 | (-14.68, 8.88, -45.88) | |
| 14:94770808 | rs28929488 | D>N | A:367 | (-6.43, 10.97, -38.05) |
| 14:94770798 | T>N | A:370 | (-6.78, 9.25, -33.76) | |
| 14:94770792 | S>N | A:372 | (-10.86, 10.38, -35.94) | |
| 14:94770780 | L>R | A:376 | (-18.70, 12.20, -43.21) | |
| 14:94770777 | A>V | A:377 | (-19.78, 13.41, -47.46) | |
| 14:94770771 | V>A | A:379 | (-21.51, 15.14, -53.10) | |
| 14:94770772 | V>F | A:379 | (-21.51, 15.14, -53.10) | |
| 14:94770762 | P>Q | A:382 | (-20.75, 20.35, -56.74) | |
| 14:94770760 | V>M | A:383 | (-22.54, 23.92, -56.99) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 14:94780738 | COSM2253210 | G>D | A:61 | (-29.51, 10.46, -15.10) |
| 14:94780729 | COSM1608093 | R>P | A:64 | (-25.30, 10.93, -16.87) |
| 14:94780730 | COSM1563032 | R>W | A:64 | (-25.30, 10.93, -16.87) |
| 14:94780400 | COSM2151408 | V>I | A:174 | (-25.00, 28.91, -26.11) |
| 14:94780373 | COSM3499300 | G>S | A:183 | (-4.98, 20.50, -46.52) |
| 14:94776287 | COSM1371786 | D>N | A:202 | (-30.84, 14.43, -60.90) |
| 14:94776221 | COSM3754193 | S>A | A:224 | (-16.68, -7.40, -55.10) |
| 14:94776112 | COSM267404 | R>Q | A:260 | (-15.85, -0.70, -37.00) |
| 14:94776106 | COSM1470747 | T>M | A:262 | (-16.51, -1.66, -44.87) |
| 14:94776089 | COSM4053224 | A>T | A:268 | (-6.98, -4.27, -47.29) |
| 14:94772437 | COSM1371783 | T>A | A:313 | (-27.00, 25.42, -13.05) |
| 14:94770782 | COSM1371778 | F>L | A:375 | (-14.61, 16.56, -41.93) |