General Structure Information
| PDB ID | 4cca |
| HGNC Gene Label(s) | STXBP2 |
| Structure Name | structure of human munc18-2 |
| Resolution | 2.6Å |
| Reference | AUTH Y.HACKMANN,S.C.GRAHAM,S.EHL,S.HOENING,K.LEHMBERG,M.ARICO,AUTH 2 D.J.OWEN,G.G.GRIFFITHSTITL SYNTAXIN BINDING MECHANISM AND DISEASE-CAUSING MUTATIONS INTITL 2 MUNC18-2REF PROC.NATL.ACAD.SCI.USA V. 110 E4482 2013REFN ISSN 0027-8424PMID 24194549DOI 10.1073/PNAS.1313474110 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 542 |
| Number Of SNVs | 146 |
| Number Of Permutations | 65582 |
| Optimal Distance Threshold | 18.0 |
| K Statistic | 0.13 |
| p-value | 0.016 |
ClinVar
| Number Of Residues | 542 |
| Number Of SNVs | 3 |
| Number Of Permutations | 310 |
| Optimal Distance Threshold | 22.0 |
| K Statistic | 0.667 |
| p-value | 0.307 |
COSMIC
| Number Of Residues | 542 |
| Number Of SNVs | 4 |
| Number Of Permutations | 112 |
| Optimal Distance Threshold | 26.0 |
| K Statistic | 0.167 |
| p-value | 0.856 |
Ripley’s K Analysis Plots
ExACClinVarCOSMIC
Variant Set Comparisons
ClinVar vs. ExAC
| Number Of ExAC SNVs | 146 |
| Number Of ClinVar SNVs | 3 |
| Optimal Distance Threshold | 22.0 |
| K Statistic | 0.461 |
| p-value | 0.295 |
Cosmic vs. ExAC
| Number Of ExAC SNVs | 146 |
| Number Of COSMIC SNVs | 4 |
| Optimal Distance Threshold | 21.0 |
| K Statistic | -0.186 |
| p-value | 0.813 |
Pathogenic Proximity Analysis
ClinVar PathProx Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 19:7703623 | rs146165014 | G>R | A:17 | (-15.65, 10.11, -7.11) |
| 19:7703629 | I>V | A:19 | (-12.72, 6.23, -11.94) | |
| 19:7703633 | R>Q | A:20 | (-11.25, 4.89, -5.22) | |
| 19:7703635 | S>R | A:21 | (-17.39, 5.21, -7.03) | |
| 19:7703638 | rs575143221 | V>I | A:22 | (-17.90, 2.96, -10.50) |
| 19:7703643 | K>N | A:23 | (-12.77, -0.11, -7.92) | |
| 19:7703646 | K>N | A:24 | (-15.28, -3.83, -9.78) | |
| 19:7703651 | G>A | A:26 | (-13.62, -8.45, -11.01) | |
| 19:7703914 | M>V | A:33 | (-14.22, 11.05, -22.03) | |
| 19:7703923 | P>S | A:36 | (-15.55, 19.30, -22.74) | |
| 19:7703924 | P>R | A:36 | (-15.55, 19.30, -22.74) | |
| 19:7703933 | rs200306463 COSM1003332 CM106813 |
R>H | A:39 | (-10.66, 19.91, -23.45) |
| 19:7703948 | C>Y | A:44 | (-5.13, 16.46, -13.29) | |
| 19:7703984 | rs138007892 | T>I | A:56 | (-9.95, -1.65, -20.27) |
| 19:7704631 | rs368283130 | N>D | A:62 | (-17.50, 13.03, -30.38) |
| 19:7704632 | rs540968221 | N>S | A:62 | (-17.50, 13.03, -30.38) |
| 19:7704637 | COSM1003333 | R>W | A:64 | (-17.53, 3.68, -35.86) |
| 19:7704638 | COSM4082866 | R>Q | A:64 | (-17.53, 3.68, -35.86) |
| 19:7704641 | rs141717050 | R>Q | A:65 | (-17.54, 4.59, -29.64) |
| 19:7704652 | rs532380776 COSM1711707 |
P>A | A:69 | (-21.28, -6.39, -25.16) |
| 19:7704655 | S>G | A:70 | (-17.97, -7.99, -21.97) | |
| 19:7704689 | E>V | A:81 | (-28.61, 18.95, -27.04) | |
| 19:7704692 | COSM440641 | K>R | A:82 | (-23.19, 18.13, -29.89) |
| 19:7705618 | S>L | A:83 | (-22.89, 15.08, -24.96) | |
| 19:7705641 | F>L | A:91 | (-27.17, 2.30, -25.46) | |
| 19:7705643 | F>L | A:91 | (-27.17, 2.30, -25.46) | |
| 19:7705645 | Q>L | A:92 | (-32.42, 4.61, -29.58) | |
| 19:7705666 | rs535808030 | Y>C | A:99 | (-21.01, -0.04, -24.96) |
| 19:7705692 | COSM176967 | D>N | A:108 | (-23.01, 20.50, -14.53) |
| 19:7705792 | P>H | A:111 | (-30.81, 20.42, -18.48) | |
| 19:7705794 | rs368824770 | E>K | A:112 | (-35.02, 18.98, -17.52) |
| 19:7705796 | E>D | A:112 | (-35.02, 18.98, -17.52) | |
| 19:7705797 | P>S | A:113 | (-35.13, 19.87, -21.07) | |
| 19:7705798 | P>L | A:113 | (-35.13, 19.87, -21.07) | |
| 19:7705813 | L>P | A:118 | (-31.89, 10.19, -21.09) | |
| 19:7705818 | rs140745219 | R>C | A:120 | (-37.88, 8.07, -23.45) |
| 19:7705819 | COSM3971364 COSM3971365 |
R>H | A:120 | (-37.88, 8.07, -23.45) |
| 19:7705825 | rs144914451 | R>H | A:122 | (-33.78, 2.74, -24.84) |
| 19:7705835 | K>N | A:125 | (-33.28, 0.38, -19.75) | |
| 19:7705839 | V>M | A:127 | (-29.26, 3.72, -17.07) | |
| 19:7705863 | L>F | A:135 | (-15.35, 19.13, -11.47) | |
| 19:7705872 | L>F | A:138 | (-9.06, 22.97, -17.48) | |
| 19:7705881 | rs147948442 | E>K | A:141 | (-0.61, 26.17, -12.80) |
| 19:7706631 | Y>S | A:157 | (-16.51, 41.83, -24.50) | |
| 19:7706655 | R>H | A:165 | (-23.82, 40.52, -22.53) | |
| 19:7706658 | rs181216956 | T>M | A:166 | (-27.14, 37.45, -20.71) |
| 19:7706660 | R>W | A:167 | (-26.39, 30.80, -21.85) | |
| 19:7706664 | rs369683019 | Q>R | A:168 | (-20.95, 33.45, -21.96) |
| 19:7706729 | rs370053399 | R>C | A:190 | (-14.57, 42.77, -2.79) |
| 19:7706921 | G>R | A:194 | (-18.00, 50.81, -13.47) | |
| 19:7706924 | P>S | A:195 | (-17.01, 48.07, -15.54) | |
| 19:7706928 | E>G | A:196 | (-22.78, 46.64, -17.30) | |
| 19:7706931 | D>V | A:197 | (-19.70, 43.13, -17.69) | |
| 19:7706933 | T>P | A:198 | (-17.38, 43.61, -13.67) | |
| 19:7706944 | rs188212047 | L>F | A:201 | (-19.67, 37.70, -13.68) |
| 19:7706951 | rs373450263 | A>T | A:204 | (-24.58, 36.00, -11.48) |
| 19:7706954 | rs144586070 | V>I | A:205 | (-20.94, 34.25, -9.05) |
| 19:7706967 | rs121918541 CM096291 |
L>Q | A:209 | (-21.98, 30.61, -4.19) |
| 19:7706972 | A>T | A:211 | (-27.61, 27.32, -4.88) | |
| 19:7706982 | A>V | A:214 | (-29.03, 26.32, 0.24) | |
| 19:7706987 | T>A | A:216 | (-24.33, 22.24, 1.67) | |
| 19:7706996 | L>M | A:219 | (-20.16, 26.00, 1.62) | |
| 19:7707002 | rs201649843 | E>K | A:221 | (-19.29, 27.43, 8.37) |
| 19:7707104 | rs372973081 COSM3541411 |
R>S | A:227 | (-10.38, 36.28, 7.23) |
| 19:7707119 | I>L | A:232 | (-15.50, 39.53, -10.49) | |
| 19:7707123 | rs373830051 | M>T | A:233 | (-10.10, 43.07, -12.61) |
| 19:7707128 | R>W | A:235 | (-7.83, 42.09, -19.30) | |
| 19:7707129 | R>Q | A:235 | (-7.83, 42.09, -19.30) | |
| 19:7707143 | COSM3404780 | V>M | A:240 | (-0.62, 47.90, -19.85) |
| 19:7707168 | T>M | A:248 | (9.36, 36.36, -15.71) | |
| 19:7707176 | A>P | A:251 | (5.86, 35.03, -19.17) | |
| 19:7707201 | I>T | A:259 | (5.65, 26.87, -25.96) | |
| 19:7707209 | COSM3541412 | D>N | A:262 | (1.85, 23.45, -22.77) |
| 19:7707215 | Y>H | A:264 | (10.87, 23.71, -25.61) | |
| 19:7707317 | Y>C | A:266 | (15.41, 21.20, -27.31) | |
| 19:7707319 | E>K | A:267 | (17.10, 19.81, -32.18) | |
| 19:7707343 | COSM3378887 | R>W | A:275 | (17.75, 14.58, -31.27) |
| 19:7707355 | V>I | A:279 | (10.19, 18.76, -22.72) | |
| 19:7707360 | rs543839901 | L>F | A:280 | (4.46, 18.39, -21.09) |
| 19:7707362 | L>P | A:281 | (7.20, 23.29, -20.21) | |
| 19:7707367 | COSM3893902 | E>K | A:283 | (2.86, 21.13, -12.19) |
| 19:7707373 | D>N | A:285 | (8.90, 19.32, -14.67) | |
| 19:7707394 | COSM39646 | R>C | A:292 | (6.13, 27.86, -12.52) |
| 19:7707395 | COSM1397645 CM096292 |
R>H | A:292 | (6.13, 27.86, -12.52) |
| 19:7707659 | T>S | A:304 | (24.73, 25.68, -12.39) | |
| 19:7707660 | rs200135215 | T>M | A:304 | (24.73, 25.68, -12.39) |
| 19:7707662 | E>K | A:305 | (22.61, 26.54, -7.31) | |
| 19:7707663 | rs370890802 | E>G | A:305 | (22.61, 26.54, -7.31) |
| 19:7707683 | E>Q | A:312 | (29.06, 17.01, -5.91) | |
| 19:7707692 | R>G | A:315 | (28.93, 11.64, -5.75) | |
| 19:7707693 | R>T | A:315 | (28.93, 11.64, -5.75) | |
| 19:7707897 | L>P | A:330 | (33.44, 7.65, -16.09) | |
| 19:7707909 | P>L | A:334 | (24.99, 5.40, -17.64) | |
| 19:7707912 | Q>R | A:335 | (22.96, 4.63, -13.26) | |
| 19:7707932 | K>E | A:342 | (14.36, 15.36, -15.77) | |
| 19:7708057 | T>A | A:345 | (15.45, 20.40, -20.42) | |
| 19:7708058 | rs117761837 | T>M | A:345 | (15.45, 20.40, -20.42) |
| 19:7708061 | H>L | A:346 | (14.48, 23.26, -17.79) | |
| 19:7708072 | A>T | A:350 | (17.19, 29.47, -20.62) | |
| 19:7708081 | C>R | A:353 | (14.60, 32.54, -23.62) | |
| 19:7708086 | M>I | A:354 | (18.97, 35.22, -23.45) | |
| 19:7708091 | H>R | A:356 | (14.14, 34.00, -29.58) | |
| 19:7708097 | K>R | A:358 | (18.65, 39.29, -28.46) | |
| 19:7708103 | S>L | A:360 | (14.46, 43.54, -31.90) | |
| 19:7708123 | V>M | A:367 | (10.32, 51.55, -26.34) | |
| 19:7709512 | G>S | A:374 | (6.01, 56.68, -17.70) | |
| 19:7709513 | G>V | A:374 | (6.01, 56.68, -17.70) | |
| 19:7709518 | rs373455789 | D>N | A:376 | (13.28, 57.10, -17.92) |
| 19:7709521 | rs199913678 | A>T | A:377 | (15.50, 53.91, -16.02) |
| 19:7709528 | G>E | A:379 | (12.98, 58.01, -12.98) | |
| 19:7709548 | rs535236814 | M>V | A:386 | (4.93, 60.77, -30.79) |
| 19:7709560 | V>I | A:390 | (8.63, 57.62, -34.50) | |
| 19:7709576 | D>G | A:395 | (11.78, 49.58, -38.16) | |
| 19:7709578 | A>T | A:396 | (11.12, 47.40, -42.00) | |
| 19:7709579 | A>V | A:396 | (11.12, 47.40, -42.00) | |
| 19:7709584 | V>M | A:398 | (10.07, 45.62, -35.91) | |
| 19:7709590 | A>T | A:400 | (3.22, 43.47, -37.38) | |
| 19:7709596 | rs114628602 | D>N | A:402 | (6.29, 43.42, -32.20) |
| 19:7709602 | I>V | A:404 | (0.01, 46.08, -33.25) | |
| 19:7709605 | R>W | A:405 | (3.33, 43.43, -28.11) | |
| 19:7709606 | R>Q | A:405 | (3.33, 43.43, -28.11) | |
| 19:7709617 | L>F | A:409 | (2.05, 49.62, -24.54) | |
| 19:7709633 | rs202199284 | R>Q | A:414 | (-0.67, 60.81, -25.29) |
| 19:7710104 | rs150072458 | A>D | A:423 | (-4.65, 57.28, -39.37) |
| 19:7710122 | rs199924392 | A>V | A:429 | (3.52, 51.96, -38.91) |
| 19:7710140 | S>N | A:435 | (-6.54, 48.87, -38.86) | |
| 19:7711148 | S>C | A:457 | (-10.64, 56.57, -19.36) | |
| 19:7711151 | S>T | A:458 | (-11.79, 52.67, -17.70) | |
| 19:7711153 | rs142105943 | R>W | A:459 | (-5.29, 52.71, -17.79) |
| 19:7711163 | rs573587268 COSM1711710 |
P>L | A:462 | (0.03, 50.06, -11.59) |
| 19:7711171 | rs542557411 COSM1003338 |
R>C | A:465 | (5.27, 48.36, -6.08) |
| 19:7711172 | R>P | A:465 | (5.27, 48.36, -6.08) | |
| 19:7711174 | rs146685108 | M>L | A:466 | (10.43, 53.48, -4.19) |
| 19:7711175 | rs376908459 | M>T | A:466 | (10.43, 53.48, -4.19) |
| 19:7711178 | E>G | A:467 | (10.69, 47.94, -4.64) | |
| 19:7711181 | rs572516987 | P>L | A:468 | (15.50, 47.73, -5.86) |
| 19:7711198 | R>C | A:474 | (11.17, 49.95, -15.24) | |
| 19:7711199 | R>L | A:474 | (11.17, 49.95, -15.24) | |
| 19:7711222 | V>I | A:482 | (-6.25, 44.34, -6.47) | |
| 19:7712051 | rs199839827 | A>T | A:486 | (-7.37, 41.85, -0.65) |
| 19:7712054 | rs150174842 | V>M | A:487 | (-3.92, 39.72, 1.72) |
| 19:7712057 | E>K | A:488 | (-2.97, 43.79, 3.85) | |
| 19:7712064 | rs189009033 | R>Q | A:490 | (-3.93, 47.85, 2.20) |
| 19:7712079 | L>R | A:495 | (-12.35, 51.62, -6.84) | |
| 19:7712085 | P>L | A:497 | (-18.01, 47.26, -4.73) | |
| 19:7712096 | D>N | A:501 | (-21.76, 42.89, 4.06) | |
| 19:7712290 | A>V | A:530 | (-7.92, 25.81, 7.36) | |
| 19:7712293 | G>A | A:531 | (-6.96, 28.84, 5.64) | |
| 19:7712298 | R>W | A:533 | (-8.95, 29.01, -0.43) | |
| 19:7712299 | rs147455069 | R>Q | A:533 | (-8.95, 29.01, -0.43) |
| 19:7712304 | rs370240434 | I>V | A:535 | (-11.08, 32.72, -5.43) |
| 19:7712307 | rs374719886 | V>M | A:536 | (-8.44, 36.82, -8.61) |
| 19:7712322 | rs61736587 | G>S | A:541 | (-8.24, 36.50, -20.09) |
| 19:7712349 | A>T | A:550 | (-0.79, 34.78, -7.69) | |
| 19:7712355 | E>K | A:552 | (4.91, 37.13, -6.44) | |
| 19:7712364 | rs61736586 | R>G | A:555 | (4.53, 33.73, -0.69) |
| 19:7712373 | COSM475480 | E>K | A:558 | (4.90, 33.49, 4.76) |
| 19:7712375 | E>D | A:558 | (4.90, 33.49, 4.76) | |
| 19:7712377 | rs552459149 | G>V | A:559 | (0.65, 30.87, 4.05) |
| 19:7712382 | rs202167383 | W>R | A:561 | (-5.16, 35.37, 2.75) |
| 19:7712383 | rs537825002 | W>S | A:561 | (-5.16, 35.37, 2.75) |
| 19:7712614 | rs375332778 COSM1481677 |
S>F | A:567 | (-9.62, 33.29, -16.75) |
| 19:7712637 | rs201481880 | R>C | A:575 | (-4.65, 32.70, -26.79) |
| 19:7712649 | D>Y | A:579 | (-8.59, 37.47, -28.77) | |
| 19:7712668 | K>R | A:585 | (-13.61, 40.06, -38.11) | |
| 19:7712673 | L>V | A:587 | (-15.64, 34.53, -36.83) | |
| 19:7712683 | I>T | A:590 | (-15.98, 31.62, -32.35) | |
| 19:7712686 | rs150701487 | A>D | A:591 | (-18.18, 28.04, -29.69) |
[+] ClinVar Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 19:7706967 | rs121918541 | L>Q | A:209 | (-21.98, 30.61, -4.19) |
| 19:7711208 | rs121918540 | P>L | A:477 | (1.17, 43.02, -12.62) |
| 19:7712322 | rs61736587 | G>S | A:541 | (-8.24, 36.50, -20.09) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 19:7703933 | COSM1003332 | R>H | A:39 | (-10.66, 19.91, -23.45) |
| 19:7704637 | COSM1003333 | R>W | A:64 | (-17.53, 3.68, -35.86) |
| 19:7707343 | COSM3378887 | R>W | A:275 | (17.75, 14.58, -31.27) |
| 19:7707409 | COSM1680578 | A>T | A:297 | (18.79, 37.09, -15.09) |