General Structure Information
| PDB ID | 2gjx |
| HGNC Gene Label(s) | HEXB |
| Structure Name | crystallographic structure of human beta-hexosaminidase a |
| Resolution | 2.8Å |
| Reference | AUTH M.J.LEMIEUX,B.L.MARK,M.M.CHERNEY,S.G.WITHERS,D.J.MAHURAN,AUTH 2 M.N.G.JAMESTITL CRYSTALLOGRAPHIC STRUCTURE OF HUMAN BETA-HEXOSAMINIDASE A:TITL 2 INTERPRETATION OF TAY-SACHS MUTATIONS AND LOSS OF GM2TITL 3 GANGLIOSIDE HYDROLYSISREF J.MOL.BIOL. V. 359 913 2006REFN ISSN 0022-2836PMID 16698036DOI 10.1016/J.JMB.2006.04.004 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 480 |
| Number Of SNVs | 136 |
| Number Of Permutations | 72550 |
| Optimal Distance Threshold | 6.0 |
| K Statistic | 0.008 |
| p-value | 0.838 |
ClinVar
| Number Of Residues | 480 |
| Number Of SNVs | 9 |
| Number Of Permutations | 6846 |
| Optimal Distance Threshold | 17.0 |
| K Statistic | 0.389 |
| p-value | 0.036 |
COSMIC
| Number Of Residues | 480 |
| Number Of SNVs | 3 |
| Number Of Permutations | 1 |
| Optimal Distance Threshold | 13.0 |
| K Statistic | 0.333 |
| p-value | 1.0 |
Ripley’s K Analysis Plots
ExACClinVarCOSMIC
Variant Set Comparisons
ClinVar vs. ExAC
| Number Of ExAC SNVs | 136 |
| Number Of ClinVar SNVs | 9 |
| Optimal Distance Threshold | 17.0 |
| K Statistic | 0.232 |
| p-value | 0.035 |
Cosmic vs. ExAC
Pathogenic Proximity Analysis
ClinVar PathProx Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 5:73981246 | P>L | G:54 | (224.79, -44.99, 29.28) | |
| 5:73981249 | A>V | G:55 | (223.35, -48.15, 31.54) | |
| 5:73981252 | rs368384256 | L>Q | G:56 | (223.76, -50.43, 28.28) |
| 5:73981270 | rs820878 | L>S | G:62 | (228.31, -51.99, 18.63) |
| 5:73981272 | V>M | G:63 | (228.49, -48.79, 21.17) | |
| 5:73981276 | K>R | G:64 | (228.86, -45.90, 17.27) | |
| 5:73981282 | T>I | G:66 | (227.07, -39.28, 20.27) | |
| 5:73981291 | rs376810812 | L>P | G:69 | (221.36, -34.18, 24.13) |
| 5:73981298 | H>Q | G:71 | (214.85, -33.17, 24.51) | |
| 5:73981299 | rs147155126 | L>F | G:72 | (211.89, -37.78, 24.60) |
| 5:73981300 | L>P | G:72 | (211.89, -37.78, 24.60) | |
| 5:73981336 | rs200209801 | N>S | G:84 | (209.24, -50.60, 4.78) |
| 5:73981342 | T>M | G:86 | (207.52, -57.98, 7.32) | |
| 5:73981347 | G>S | G:88 | (201.90, -55.07, 11.52) | |
| 5:73981354 | rs369865661 | S>C | G:90 | (198.32, -57.99, 12.57) |
| 5:73985158 | H>P | G:102 | (205.45, -45.84, 26.14) | |
| 5:73985164 | Y>C | G:104 | (209.12, -51.10, 31.22) | |
| 5:73985218 | T>I | G:122 | (216.82, -31.68, 18.91) | |
| 5:73985236 | rs113678356 | L>R | G:128 | (210.04, -46.46, 12.69) |
| 5:73985244 | I>V | G:131 | (210.67, -56.60, 10.52) | |
| 5:73985250 | L>F | G:133 | (213.69, -61.20, 7.18) | |
| 5:73985263 | C>Y | G:137 | (204.62, -62.86, 14.86) | |
| 5:73985275 | COSM1070012 | P>R | G:141 | (210.58, -69.22, 20.27) |
| 5:73985280 | I>V | G:143 | (218.10, -72.91, 19.11) | |
| 5:73985290 | D>G | G:146 | (217.82, -63.71, 14.24) | |
| 5:73985296 | S>Y | G:148 | (219.72, -59.70, 15.34) | |
| 5:73989467 | rs148268937 | T>N | G:150 | (219.99, -52.46, 13.92) |
| 5:73989506 | N>S | G:163 | (216.44, -59.86, 10.41) | |
| 5:73989516 | W>C | G:166 | (211.71, -63.81, 17.96) | |
| 5:73989527 | COSM1070013 | R>Q | G:170 | (215.88, -59.18, 22.79) |
| 5:73992520 | L>V | G:172 | (212.28, -52.35, 22.35) | |
| 5:73992545 | rs200962082 | Y>C | G:180 | (218.95, -39.97, 30.41) |
| 5:73992827 | I>V | G:189 | (218.48, -40.25, 23.98) | |
| 5:73992831 | N>S | G:190 | (222.94, -39.61, 23.99) | |
| 5:73992839 | T>A | G:193 | (224.64, -46.31, 16.24) | |
| 5:73992846 | I>T | G:195 | (225.47, -52.95, 15.75) | |
| 5:73992857 | R>G | G:199 | (229.54, -65.23, 22.71) | |
| 5:73992873 | G>E | G:204 | (219.19, -69.61, 30.93) | |
| 5:73992875 | I>V | G:205 | (217.15, -69.24, 34.25) | |
| 5:73992881 | rs10805890 | I>V | G:207 | (212.81, -72.61, 37.92) |
| 5:73992882 | I>T | G:207 | (212.81, -72.61, 37.92) | |
| 5:73992894 | R>T | G:211 | (213.36, -79.74, 45.48) | |
| 5:73992912 | K>T | G:217 | (202.05, -63.62, 40.40) | |
| 5:73992915 | I>T | G:218 | (207.51, -65.75, 41.27) | |
| 5:74001050 | M>V | G:226 | (214.49, -63.74, 32.06) | |
| 5:74001057 | F>C | G:228 | (213.78, -56.52, 32.13) | |
| 5:74001071 | V>I | G:233 | (215.82, -70.50, 28.26) | |
| 5:74001072 | V>G | G:233 | (215.82, -70.50, 28.26) | |
| 5:74001089 | rs145056714 | V>I | G:239 | (208.91, -82.56, 38.63) |
| 5:74001101 | S>T | G:243 | (206.94, -82.63, 44.67) | |
| 5:74001129 | P>R | G:252 | (195.06, -87.53, 36.97) | |
| 5:74001135 | L>S | G:254 | (200.88, -88.24, 38.80) | |
| 5:74001138 | S>N | G:255 | (198.74, -84.47, 41.04) | |
| 5:74001144 | K>T | G:257 | (197.97, -88.95, 45.71) | |
| 5:74009355 | rs373979283 | Y>D | G:266 | (202.11, -75.66, 38.63) |
| 5:74009359 | T>I | G:267 | (196.54, -75.84, 36.15) | |
| 5:74009361 | rs377652697 | P>T | G:268 | (196.18, -77.04, 32.51) |
| 5:74009364 | N>H | G:269 | (195.49, -72.14, 32.13) | |
| 5:74009370 | V>I | G:271 | (201.22, -74.44, 31.87) | |
| 5:74009373 | R>C | G:272 | (197.41, -72.85, 28.68) | |
| 5:74009374 | rs533645939 COSM195989 |
R>H | G:272 | (197.41, -72.85, 28.68) |
| 5:74009376 | M>V | G:273 | (199.41, -68.23, 31.81) | |
| 5:74009383 | rs532333261 | I>T | G:275 | (204.05, -71.19, 27.51) |
| 5:74009401 | R>Q | G:281 | (207.90, -61.21, 27.53) | |
| 5:74009421 | E>Q | G:288 | (213.31, -81.23, 33.60) | |
| 5:74009426 | F>L | G:289 | (208.76, -83.76, 33.22) | |
| 5:74009446 | L>P | G:296 | (210.55, -90.56, 45.11) | |
| 5:74011355 | rs150465843 | P>A | G:308 | (211.02, -102.38, 44.65) |
| 5:74011356 | rs191887630 | P>L | G:308 | (211.02, -102.38, 44.65) |
| 5:74011358 | C>R | G:309 | (213.97, -101.44, 47.81) | |
| 5:74011385 | S>P | G:318 | (211.97, -98.38, 50.05) | |
| 5:74011392 | G>A | G:320 | (213.54, -96.11, 43.91) | |
| 5:74011395 | COSM1163405 | P>R | G:321 | (214.84, -95.85, 40.90) |
| 5:74011402 | N>K | G:323 | (211.47, -100.67, 36.86) | |
| 5:74011464 | F>S | G:344 | (205.44, -78.09, 27.42) | |
| 5:74011466 | P>T | G:345 | (205.51, -75.64, 22.43) | |
| 5:74011473 | Q>L | G:347 | (211.70, -77.62, 18.87) | |
| 5:74011478 | rs373731814 | I>V | G:349 | (211.65, -82.65, 26.14) |
| 5:74011481 | H>D | G:350 | (216.03, -81.87, 30.32) | |
| 5:74011494 | D>G | G:354 | (220.30, -86.66, 37.39) | |
| 5:74011499 | rs181898554 | V>M | G:356 | (220.85, -92.62, 38.92) |
| 5:74011514 | W>R | G:361 | (218.12, -100.16, 39.10) | |
| 5:74012414 | rs370165925 | E>A | G:362 | (222.54, -104.64, 43.20) |
| 5:74012433 | rs143375202 | Q>H | G:368 | (219.57, -109.57, 38.71) |
| 5:74012435 | D>G | G:369 | (216.15, -112.15, 35.77) | |
| 5:74012439 | F>L | G:370 | (216.26, -107.01, 31.88) | |
| 5:74012480 | E>V | G:384 | (221.50, -95.47, 33.07) | |
| 5:74012491 | I>F | G:388 | (218.18, -93.15, 28.45) | |
| 5:74012492 | rs374403696 | I>T | G:388 | (218.18, -93.15, 28.45) |
| 5:74012494 | Q>E | G:389 | (218.89, -95.70, 24.59) | |
| 5:74014133 | A>V | G:396 | (211.85, -89.39, 18.25) | |
| 5:74014140 | I>M | G:398 | (206.74, -87.44, 19.21) | |
| 5:74014150 | S>P | G:402 | (216.51, -84.48, 23.67) | |
| 5:74014159 | W>R | G:405 | (221.21, -82.88, 33.51) | |
| 5:74014163 | Q>L | G:406 | (227.27, -85.16, 32.83) | |
| 5:74014169 | rs200912276 | V>A | G:408 | (223.67, -90.14, 30.04) |
| 5:74014626 | rs199664693 | A>V | G:416 | (220.67, -88.71, 18.57) |
| 5:74014629 | rs28942073 | P>L | G:417 | (221.96, -86.94, 15.94) |
| 5:74014637 | rs77499935 | I>V | G:420 | (221.45, -81.13, 23.87) |
| 5:74014644 | E>V | G:422 | (223.16, -79.55, 30.89) | |
| 5:74014645 | E>D | G:422 | (223.16, -79.55, 30.89) | |
| 5:74014652 | K>E | G:425 | (229.48, -82.81, 37.67) | |
| 5:74014655 | D>N | G:426 | (232.21, -78.41, 39.42) | |
| 5:74014658 | S>G | G:427 | (234.81, -82.27, 38.25) | |
| 5:74014661 | A>T | G:428 | (236.79, -81.09, 35.29) | |
| 5:74014688 | T>A | G:437 | (232.57, -81.50, 21.45) | |
| 5:74014692 | A>V | G:438 | (234.33, -84.99, 20.27) | |
| 5:74014704 | P>H | G:442 | (225.14, -80.55, 21.17) | |
| 5:74014712 | L>V | G:445 | (228.03, -74.70, 30.95) | |
| 5:74014742 | S>G | G:455 | (228.53, -66.84, 49.18) | |
| 5:74014746 | rs121907982 | Y>S | G:456 | (230.09, -62.33, 52.97) |
| 5:74014751 | Q>E | G:458 | (230.97, -58.77, 45.58) | |
| 5:74014766 | rs141194538 | Y>H | G:463 | (228.66, -66.73, 39.41) |
| 5:74014772 | K>E | G:465 | (236.04, -63.40, 35.92) | |
| 5:74014773 | rs372862823 | K>R | G:465 | (236.04, -63.40, 35.92) |
| 5:74014781 | P>A | G:468 | (232.75, -70.33, 28.33) | |
| 5:74014788 | D>G | G:470 | (238.60, -71.78, 28.41) | |
| 5:74014796 | G>S | G:473 | (239.51, -78.13, 20.82) | |
| 5:74016272 | rs139129900 | Q>H | G:479 | (230.84, -74.23, 15.82) |
| 5:74016280 | COSM1438541 | I>S | G:482 | (224.50, -73.74, 22.38) |
| 5:74016283 | G>D | G:483 | (225.64, -72.32, 26.05) | |
| 5:74016288 | E>K | G:485 | (221.40, -72.91, 32.00) | |
| 5:74016307 | E>G | G:491 | (217.11, -77.75, 47.73) | |
| 5:74016327 | L>F | G:498 | (213.53, -66.51, 43.85) | |
| 5:74016469 | rs121907985 | P>S | G:504 | (221.86, -59.06, 40.47) |
| 5:74016473 | rs121907983 | R>Q | G:505 | (223.74, -64.10, 42.21) |
| 5:74016496 | L>V | G:513 | (225.79, -66.06, 27.67) | |
| 5:74016497 | L>P | G:513 | (225.79, -66.06, 27.67) | |
| 5:74016502 | S>R | G:515 | (228.33, -59.94, 25.46) | |
| 5:74016518 | COSM3856273 | R>T | G:520 | (236.42, -60.20, 31.02) |
| 5:74016524 | M>T | G:522 | (235.48, -56.04, 36.99) | |
| 5:74016526 | D>N | G:523 | (236.03, -51.12, 37.43) | |
| 5:74016532 | A>T | G:525 | (230.60, -54.03, 35.51) | |
| 5:74016545 | L>R | G:529 | (225.22, -54.45, 37.57) | |
| 5:74016548 | rs531151091 | T>R | G:530 | (224.90, -50.70, 40.16) |
| 5:74016551 | R>T | G:531 | (224.06, -47.35, 36.26) | |
| 5:74016552 | R>S | G:531 | (224.06, -47.35, 36.26) | |
| 5:74016556 | R>C | G:533 | (219.78, -53.07, 42.16) | |
| 5:74016571 | rs143635580 | E>K | G:538 | (212.98, -48.29, 39.12) |
| 5:74016944 | R>C | G:539 | (211.93, -52.16, 34.86) | |
| 5:74016945 | R>H | G:539 | (211.93, -52.16, 34.86) | |
| 5:74016951 | I>T | G:541 | (212.53, -56.81, 39.91) | |
| 5:74016956 | rs121907984 | A>T | G:543 | (217.24, -56.82, 43.38) |
| 5:74016959 | Q>K | G:544 | (220.63, -58.93, 45.97) | |
| 5:74016962 | P>S | G:545 | (222.36, -55.38, 47.09) | |
| 5:74016974 | rs398123448 | G>R | G:549 | (224.05, -47.81, 48.78) |
| 5:74016984 | N>S | G:552 | (216.92, -43.53, 42.63) |
[+] ClinVar Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 5:73981270 | rs820878 | L>S | G:62 | (228.31, -51.99, 18.63) |
| 5:73992881 | rs10805890 | I>V | G:207 | (212.81, -72.61, 37.92) |
| 5:74009356 | rs398123450 | Y>C | G:266 | (202.11, -75.66, 38.63) |
| 5:74014629 | rs28942073 | P>L | G:417 | (221.96, -86.94, 15.94) |
| 5:74014746 | rs121907982 | Y>S | G:456 | (230.09, -62.33, 52.97) |
| 5:74014754 | rs398123447 | D>Y | G:459 | (228.95, -64.27, 44.39) |
| 5:74016313 | rs794727049 | V>G | G:493 | (214.54, -71.43, 47.09) |
| 5:74016469 | rs121907985 | P>S | G:504 | (221.86, -59.06, 40.47) |
| 5:74016473 | rs121907983 | R>Q | G:505 | (223.74, -64.10, 42.21) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 5:73981270 | COSM450042 | L>S | G:62 | (228.31, -51.99, 18.63) |
| 5:74016341 | COSM1754328 | L>F | G:502 | (218.09, -64.87, 40.74) |
| 5:74016557 | COSM1132123 | R>H | G:533 | (219.78, -53.07, 42.16) |