General Structure Information
| PDB ID | 1j78 |
| HGNC Gene Label(s) | GC |
| Structure Name | crystallographic analysis of the human vitamin d binding protein |
| Resolution | 2.31Å |
| Reference | AUTH C.VERBOVEN,A.RABIJNS,M.DE MAEYER,H.VAN BAELEN,AUTH 2 R.BOUILLON,C.DE RANTERTITL A STRUCTURAL BASIS FOR THE UNIQUE BINDING FEATURESTITL 2 OF THE HUMAN VITAMIN D-BINDING PROTEIN.REF NAT.STRUCT.BIOL. V. 9 131 2002REFN ISSN 1072-8368PMID 11799400DOI 10.1038/NSB754 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 447 |
| Number Of SNVs | 126 |
| Number Of Permutations | 30250 |
| Optimal Distance Threshold | 6.0 |
| K Statistic | 0.009 |
| p-value | 0.859 |
COSMIC
| Number Of Residues | 447 |
| Number Of SNVs | 8 |
| Number Of Permutations | 4202 |
| Optimal Distance Threshold | 35.0 |
| K Statistic | 0.286 |
| p-value | 0.074 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 126 |
| Number Of COSMIC SNVs | 7 |
| Optimal Distance Threshold | 26.0 |
| K Statistic | -0.234 |
| p-value | 0.048 |
Pathogenic Proximity Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 4:72649680 | COSM3775968 COSM3775967 |
R>K | B:3 | (-15.15, -70.20, 59.73) |
| 4:72635114 | rs117925738 | R>Q | B:5 | (-20.08, -67.40, 57.32) |
| 4:72635115 | rs180820099 | R>W | B:5 | (-20.08, -67.40, 57.32) |
| 4:72635112 | D>Y | B:6 | (-17.30, -65.15, 58.35) | |
| 4:72635099 | COSM1057213 COSM1594576 |
N>S | B:10 | (-14.11, -60.89, 57.87) |
| 4:72635075 | H>R | B:18 | (-4.71, -52.66, 55.72) | |
| 4:72635069 | G>A | B:20 | (-9.34, -47.48, 55.85) | |
| 4:72635064 | COSM3605614 COSM3605613 |
E>K | B:22 | (-10.00, -42.02, 52.54) |
| 4:72635061 | D>N | B:23 | (-8.04, -45.62, 51.35) | |
| 4:72635054 | T>I | B:25 | (-14.31, -45.28, 50.26) | |
| 4:72634134 | rs375694858 | S>G | B:33 | (-17.44, -48.06, 39.01) |
| 4:72634091 | L>P | B:47 | (-23.71, -48.59, 46.50) | |
| 4:72634084 | rs141480221 | K>N | B:49 | (-22.51, -43.58, 51.47) |
| 4:72634081 | rs199843805 | E>D | B:50 | (-25.39, -47.79, 52.39) |
| 4:72634082 | E>A | B:50 | (-25.39, -47.79, 52.39) | |
| 4:72634068 | T>S | B:55 | (-18.32, -52.14, 56.75) | |
| 4:72634065 | rs372964536 | E>K | B:56 | (-17.98, -48.08, 60.07) |
| 4:72634062 | A>T | B:57 | (-21.23, -50.33, 61.68) | |
| 4:72634052 | A>V | B:60 | (-17.86, -52.82, 65.51) | |
| 4:72634039 | D>E | B:64 | (-21.32, -59.65, 66.44) | |
| 4:72634041 | D>H | B:64 | (-21.32, -59.65, 66.44) | |
| 4:72634034 | rs566666266 | D>V | B:66 | (-26.12, -60.15, 63.82) |
| 4:72634031 | C>S | B:67 | (-24.43, -57.69, 60.81) | |
| 4:72634028 | Y>C | B:68 | (-21.85, -58.60, 55.97) | |
| 4:72634022 | T>S | B:70 | (-29.41, -58.24, 58.14) | |
| 4:72634018 | R>S | B:71 | (-26.88, -53.00, 56.93) | |
| 4:72631333 | E>Q | B:81 | (-36.90, -48.85, 44.83) | |
| 4:72631329 | S>N | B:82 | (-39.04, -48.78, 40.71) | |
| 4:72631312 | V>I | B:88 | (-28.94, -52.16, 38.31) | |
| 4:72631284 | T>I | B:97 | (-39.85, -61.61, 41.15) | |
| 4:72631261 | L>F | B:105 | (-28.81, -64.66, 44.50) | |
| 4:72631251 | A>V | B:108 | (-25.24, -62.49, 41.99) | |
| 4:72631218 | rs142840177 | T>I | B:119 | (-16.91, -40.69, 27.05) |
| 4:72631216 | Y>N | B:120 | (-11.52, -39.70, 30.29) | |
| 4:72631213 | V>M | B:121 | (-11.75, -36.43, 27.59) | |
| 4:72631206 | P>L | B:123 | (-9.29, -32.16, 30.97) | |
| 4:72631207 | P>S | B:123 | (-9.29, -32.16, 30.97) | |
| 4:72631197 | D>V | B:126 | (-6.21, -24.42, 33.11) | |
| 4:72631185 | rs557587112 | E>G | B:130 | (-10.43, -24.06, 37.69) |
| 4:72631182 | rs116134435 | A>V | B:131 | (-11.76, -28.36, 39.73) |
| 4:72631169 | D>E | B:135 | (-14.29, -29.96, 45.53) | |
| 4:72631156 | A>T | B:140 | (-11.46, -37.53, 42.97) | |
| 4:72631152 | N>S | B:141 | (-14.78, -38.89, 44.17) | |
| 4:72629648 | rs149023528 | M>T | B:144 | (-11.98, -42.37, 41.25) |
| 4:72629625 | rs371509305 | G>R | B:152 | (-13.38, -51.74, 33.63) |
| 4:72629621 | rs543097543 | Q>R | B:153 | (-13.06, -54.91, 31.43) |
| 4:72629612 | L>R | B:156 | (-9.60, -53.27, 40.76) | |
| 4:72629607 | L>I | B:158 | (-4.21, -50.94, 36.89) | |
| 4:72629588 | rs575759317 | K>R | B:164 | (-2.65, -43.24, 43.53) |
| 4:72629574 | rs140278474 | M>V | B:169 | (-0.30, -35.42, 38.54) |
| 4:72629570 | V>A | B:170 | (-3.51, -33.16, 40.09) | |
| 4:72629547 | rs557326400 | S>C | B:178 | (5.51, -24.84, 37.29) |
| 4:72629203 | H>R | B:192 | (3.62, -47.68, 31.43) | |
| 4:72629204 | H>Y | B:192 | (3.62, -47.68, 31.43) | |
| 4:72629199 | L>F | B:193 | (0.20, -46.85, 34.25) | |
| 4:72629201 | L>V | B:193 | (0.20, -46.85, 34.25) | |
| 4:72629192 | L>V | B:196 | (-1.27, -50.82, 30.74) | |
| 4:72629158 | Y>F | B:207 | (-11.64, -62.59, 25.97) | |
| 4:72629152 | rs374208796 | A>G | B:209 | (-17.63, -59.99, 23.87) |
| 4:72629153 | A>T | B:209 | (-17.63, -59.99, 23.87) | |
| 4:72629147 | G>R | B:211 | (-14.65, -65.19, 23.89) | |
| 4:72629134 | S>L | B:215 | (-11.04, -64.22, 20.48) | |
| 4:72629132 | R>G | B:216 | (-8.28, -69.11, 18.14) | |
| 4:72629128 | L>P | B:217 | (-11.75, -66.80, 14.79) | |
| 4:72623886 | N>S | B:219 | (-7.13, -62.39, 17.12) | |
| 4:72623880 | I>T | B:221 | (-9.84, -62.75, 11.06) | |
| 4:72623863 | V>L | B:227 | (-0.13, -60.31, 6.95) | |
| 4:72623859 | P>R | B:228 | (-2.25, -60.64, 3.39) | |
| 4:72623854 | A>T | B:230 | (1.59, -64.73, 5.01) | |
| 4:72623842 | COSM3605606 COSM3605605 |
D>N | B:234 | (3.61, -67.09, 9.73) |
| 4:72623839 | rs143184570 | V>I | B:235 | (-0.38, -65.89, 11.88) |
| 4:72623829 | rs182805109 | L>P | B:238 | (0.97, -64.96, 16.67) |
| 4:72623788 | COSM361262 | S>T | B:252 | (-6.18, -61.61, 36.62) |
| 4:72623784 | A>V | B:253 | (-6.20, -59.49, 39.71) | |
| 4:72623785 | A>S | B:253 | (-6.20, -59.49, 39.71) | |
| 4:72623779 | E>Q | B:255 | (-1.14, -54.40, 38.83) | |
| 4:72623772 | C>Y | B:257 | (-0.42, -59.80, 33.49) | |
| 4:72623766 | A>D | B:259 | (3.16, -56.03, 31.24) | |
| 4:72623759 | E>D | B:261 | (2.58, -62.03, 29.10) | |
| 4:72622628 | P>S | B:263 | (7.03, -58.44, 26.35) | |
| 4:72622621 | H>R | B:265 | (3.03, -61.48, 21.72) | |
| 4:72622616 | COSM1057208 COSM1594580 |
V>I | B:267 | (9.61, -61.22, 20.42) |
| 4:72622601 | rs41265647 | N>D | B:272 | (7.14, -64.73, 12.87) |
| 4:72622597 | L>S | B:273 | (5.49, -60.84, 10.98) | |
| 4:72622565 | COSM1057206 COSM1154366 |
C>R | B:284 | (8.89, -53.99, 15.14) |
| 4:72622561 | rs370244436 | Q>P | B:285 | (11.27, -49.96, 13.89) |
| 4:72622552 | T>I | B:288 | (8.11, -50.13, 23.84) | |
| 4:72622549 | A>V | B:289 | (6.32, -53.68, 23.63) | |
| 4:72622541 | rs148501037 | V>I | B:292 | (4.96, -53.06, 19.13) |
| 4:72622531 | rs144667072 | C>F | B:295 | (1.28, -50.60, 16.11) |
| 4:72622526 | COSM123328 | Y>H | B:297 | (-4.47, -56.24, 18.75) |
| 4:72622518 | M>I | B:299 | (-2.27, -52.60, 11.78) | |
| 4:72622519 | rs201290152 | M>T | B:299 | (-2.27, -52.60, 11.78) |
| 4:72622508 | Q>E | B:303 | (-5.11, -53.54, -0.33) | |
| 4:72622505 | L>V | B:304 | (-6.97, -57.62, 0.72) | |
| 4:72622499 | rs375201505 COSM3661186 COSM3661185 |
E>K | B:306 | (-7.56, -60.98, -4.44) |
| 4:72622489 | D>V | B:309 | (-11.94, -68.23, -4.25) | |
| 4:72622474 | T>I | B:314 | (-16.61, -80.26, 2.26) | |
| 4:72622470 | N>K | B:315 | (-14.30, -82.83, 4.80) | |
| 4:72622463 | rs371054565 | V>L | B:318 | (-14.18, -80.48, 9.75) |
| 4:72622444 | T>I | B:324 | (-9.07, -76.53, 14.46) | |
| 4:72622445 | T>A | B:324 | (-9.07, -76.53, 14.46) | |
| 4:72620819 | T>I | B:331 | (-10.53, -68.78, 8.66) | |
| 4:72620810 | L>Q | B:334 | (-12.25, -66.08, 3.82) | |
| 4:72620808 | rs117492633 | S>G | B:335 | (-9.75, -63.45, 5.93) |
| 4:72620789 | rs139133782 | P>L | B:341 | (-15.18, -56.09, 8.12) |
| 4:72620774 | S>N | B:346 | (-16.62, -63.14, 13.16) | |
| 4:72620763 | rs568820346 COSM1540896 COSM1540895 |
E>Q | B:350 | (-20.55, -68.57, 14.96) |
| 4:72620754 | COSM3409462 COSM3409461 |
L>V | B:353 | (-17.62, -73.12, 10.70) |
| 4:72620745 | COSM123327 | L>V | B:356 | (-20.08, -77.44, 7.98) |
| 4:72620741 | G>V | B:357 | (-20.90, -79.96, 11.98) | |
| 4:72620726 | rs143944893 | V>G | B:362 | (-24.88, -87.83, 9.94) |
| 4:72620712 | T>A | B:367 | (-24.46, -87.06, 1.41) | |
| 4:72620697 | COSM3392949 COSM3392948 |
K>E | B:372 | (-25.22, -78.03, 3.91) |
| 4:72620212 | rs142448358 | K>R | B:377 | (-22.37, -70.80, -0.23) |
| 4:72620162 | rs150474816 | Y>H | B:394 | (-15.49, -45.89, 5.84) |
| 4:72620149 | rs369671547 | T>I | B:398 | (-12.70, -38.92, 2.82) |
| 4:72620143 | rs140591638 | T>I | B:400 | (-16.57, -35.82, 3.25) |
| 4:72620128 | K>R | B:405 | (-18.78, -41.59, -3.52) | |
| 4:72618365 | L>P | B:406 | (-23.63, -42.95, 0.21) | |
| 4:72618356 | R>Q | B:409 | (-23.48, -46.14, -4.46) | |
| 4:72618351 | COSM3767969 COSM3767968 |
K>E | B:411 | (-29.19, -40.08, -5.77) |
| 4:72618334 | rs7041 | D>E | B:416 | (-39.24, -40.58, -6.54) |
| 4:72618333 | A>P | B:417 | (-36.38, -39.58, -3.05) | |
| 4:72618327 | P>A | B:419 | (-33.99, -34.27, -0.65) | |
| 4:72618314 | A>E | B:423 | (-30.38, -37.29, 4.19) | |
| 4:72618296 | rs9016 | H>R | B:429 | (-25.82, -46.87, 5.24) |
| 4:72618297 | rs3737553 | H>Y | B:429 | (-25.82, -46.87, 5.24) |
| 4:72618290 | D>G | B:431 | (-23.68, -43.72, 11.99) | |
| 4:72618281 | S>Y | B:434 | (-18.47, -44.92, 11.51) | |
| 4:72618273 | C>R | B:437 | (-16.54, -50.56, 8.50) | |
| 4:72618267 | I>V | B:439 | (-9.86, -53.87, 11.95) | |
| 4:72618263 | N>T | B:440 | (-10.55, -52.23, 15.66) | |
| 4:72618255 | P>S | B:443 | (-18.07, -56.28, 18.95) | |
| 4:72618245 | rs558979480 | C>Y | B:446 | (-21.77, -54.11, 15.28) |
| 4:72618246 | C>G | B:446 | (-21.77, -54.11, 15.28) | |
| 4:72611922 | rs191456559 | I>L | B:450 | (-24.66, -56.20, 11.18) |
| 4:72611916 | A>T | B:452 | (-30.49, -54.43, 10.68) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 4:72634121 | COSM140486 | P>L | B:37 | (-20.75, -49.90, 33.59) |
| 4:72634050 | COSM1619032 | E>Q | B:61 | (-16.64, -53.81, 69.89) |
| 4:72629165 | COSM1430857 | S>P | B:205 | (-13.58, -55.34, 26.21) |
| 4:72623842 | COSM3605605 | D>N | B:234 | (3.61, -67.09, 9.73) |
| 4:72623787 | COSM195771 | S>F | B:252 | (-6.18, -61.61, 36.62) |
| 4:72620697 | COSM3392949 | K>E | B:372 | (-25.22, -78.03, 3.91) |
| 4:72618334 | COSM149688 | D>E | B:416 | (-39.24, -40.58, -6.54) |
| 4:72618323 | COSM4003131 | T>K | B:420 | (-35.13, -34.95, 3.49) |