General Structure Information
| PDB ID | 3thc |
| HGNC Gene Label(s) | GLB1 |
| Structure Name | crystal structure of human beta-galactosidase in complex with galactose |
| Resolution | 1.8Å |
| Reference | AUTH U.OHTO,K.USUI,T.OCHI,K.YUKI,Y.SATOW,T.SHIMIZUTITL CRYSTAL STRUCTURE OF HUMAN BETA-GALACTOSIDASE: STRUCTURALTITL 2 BASIS OF GM1 GANGLIOSIDOSIS AND MORQUIO B DISEASESREF J.BIOL.CHEM. V. 287 1801 2012REFN ISSN 0021-9258PMID 22128166DOI 10.1074/JBC.M111.293795 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 605 |
| Number Of SNVs | 135 |
| Number Of Permutations | 65963 |
| Optimal Distance Threshold | 10.0 |
| K Statistic | 0.028 |
| p-value | 0.345 |
ClinVar
| Number Of Residues | 605 |
| Number Of SNVs | 29 |
| Number Of Permutations | 20288 |
| Optimal Distance Threshold | 22.0 |
| K Statistic | 0.355 |
| p-value | 0.009 |
COSMIC
| Number Of Residues | 605 |
| Number Of SNVs | 6 |
| Number Of Permutations | 2615 |
| Optimal Distance Threshold | 24.0 |
| K Statistic | 0.467 |
| p-value | 0.449 |
Ripley’s K Analysis Plots
ExACClinVarCOSMIC
Variant Set Comparisons
ClinVar vs. ExAC
| Number Of ExAC SNVs | 135 |
| Number Of ClinVar SNVs | 29 |
| Optimal Distance Threshold | 25.0 |
| K Statistic | 0.148 |
| p-value | 0.012 |
Cosmic vs. ExAC
| Number Of ExAC SNVs | 135 |
| Number Of COSMIC SNVs | 4 |
| Optimal Distance Threshold | 24.0 |
| K Statistic | 0.387 |
| p-value | 0.319 |
Pathogenic Proximity Analysis
ClinVar PathProx Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 3:33114174 | COSM480030 COSM3660490 |
Y>C | A:36 | (8.52, -15.92, -14.99) |
| 3:33114168 | R>Q | A:38 | (13.21, -23.96, -14.47) | |
| 3:33114135 | COSM4116938 COSM4116937 CM056964 |
R>H | A:49 | (11.06, -22.38, -0.71) |
| 3:33114136 | rs72555358 | R>C | A:49 | (11.06, -22.38, -0.71) |
| 3:33114120 | rs143423935 | S>N | A:54 | (6.06, -10.79, 9.71) |
| 3:33114105 | rs72555392 | R>H | A:59 | (3.83, -2.96, 15.55) |
| 3:33114106 | COSM3915764 COSM3915763 CM051078 |
R>C | A:59 | (3.83, -2.96, 15.55) |
| 3:33114103 | V>M | A:60 | (9.89, -3.92, 18.12) | |
| 3:33114096 | R>H | A:62 | (17.41, 0.15, 17.61) | |
| 3:33114097 | R>C | A:62 | (17.41, 0.15, 17.61) | |
| 3:33114092 | F>L | A:63 | (16.94, -3.13, 24.04) | |
| 3:33114090 | Y>C | A:64 | (14.15, -6.29, 23.15) | |
| 3:33114078 | rs572237881 CM094652 |
R>Q | A:68 | (12.32, -9.92, 19.39) |
| 3:33114079 | rs72555370 | R>W | A:68 | (12.32, -9.92, 19.39) |
| 3:33114065 | M>I | A:72 | (12.53, -14.79, 13.23) | |
| 3:33114063 | K>R | A:73 | (18.33, -17.35, 12.05) | |
| 3:33114046 | rs553660803 COSM1422427 |
A>T | A:79 | (13.14, -14.35, 5.57) |
| 3:33114043 | I>F | A:80 | (12.39, -10.83, 7.27) | |
| 3:33114039 | Q>L | A:81 | (7.39, -9.63, 5.16) | |
| 3:33114036 | rs118203930 | T>M | A:82 | (8.65, -5.14, 6.86) |
| 3:33110437 | P>T | A:91 | (5.71, 13.61, 10.90) | |
| 3:33110412 | S>C | A:99 | (16.73, 7.76, 14.05) | |
| 3:33110404 | H>D | A:102 | (11.73, 5.98, 14.05) | |
| 3:33110398 | V>M | A:104 | (14.48, 1.26, 8.33) | |
| 3:33110382 | COSM4116936 COSM4116935 |
R>P | A:109 | (22.15, -2.13, 8.07) |
| 3:33110383 | rs35289681 | R>W | A:109 | (22.15, -2.13, 8.07) |
| 3:33110334 | Y>S | A:125 | (-2.60, 1.08, 2.49) | |
| 3:33109778 | G>V | A:134 | (0.28, 4.90, 7.14) | |
| 3:33109764 | L>M | A:139 | (-2.53, 13.48, 3.14) | |
| 3:33109736 | R>H | A:148 | (-5.47, 3.35, -1.58) | |
| 3:33109733 | S>F | A:149 | (-5.64, 7.82, -6.17) | |
| 3:33109728 | rs375582374 CM042715 |
D>N | A:151 | (-5.53, 12.83, -6.07) |
| 3:33107025 | W>L | A:161 | (8.15, 8.59, 1.94) | |
| 3:33106962 | T>I | A:182 | (11.04, -8.82, -2.81) | |
| 3:33099745 | G>D | A:190 | (-8.49, -4.85, -4.53) | |
| 3:33099730 | C>Y | A:195 | (-9.89, 0.55, -9.56) | |
| 3:33099712 | rs189115557 | R>H | A:201 | (-0.35, 2.28, -14.69) |
| 3:33099713 | rs72555360 | R>C | A:201 | (-0.35, 2.28, -14.69) |
| 3:33099697 | rs552709460 | R>H | A:206 | (8.80, 7.38, -9.59) |
| 3:33099698 | R>C | A:206 | (8.80, 7.38, -9.59) | |
| 3:33099691 | rs111840209 | R>H | A:208 | (11.29, -0.67, -11.67) |
| 3:33099692 | rs72555366 | R>C | A:208 | (11.29, -0.67, -11.67) |
| 3:33099688 | H>R | A:209 | (13.47, 6.69, -11.02) | |
| 3:33099680 | COSM3660489 COSM3660488 |
G>R | A:212 | (15.26, -0.39, -10.83) |
| 3:33099676 | D>V | A:213 | (14.85, -2.13, -14.34) | |
| 3:33099677 | D>N | A:213 | (14.85, -2.13, -14.34) | |
| 3:33099671 | V>M | A:215 | (13.73, -4.99, -8.26) | |
| 3:33099646 | A>G | A:223 | (-7.62, -15.55, -2.98) | |
| 3:33099647 | A>T | A:223 | (-7.62, -15.55, -2.98) | |
| 3:33099643 | rs555982301 | H>R | A:224 | (-11.82, -14.51, -5.42) |
| 3:33099617 | L>M | A:233 | (-0.34, -4.15, -12.73) | |
| 3:33099611 | G>S | A:235 | (4.75, -6.01, -14.04) | |
| 3:33099602 | T>A | A:238 | (0.28, -11.58, -8.85) | |
| 3:33099598 | T>M | A:239 | (0.90, -12.34, -4.65) | |
| 3:33095013 | S>R | A:254 | (-6.24, -17.52, -7.74) | |
| 3:33095004 | K>N | A:257 | (-6.79, -16.35, -13.41) | |
| 3:33095003 | rs372483857 | C>R | A:258 | (-2.80, -13.89, -12.54) |
| 3:33094993 | rs200050465 | K>R | A:261 | (4.87, -19.32, -16.28) |
| 3:33093489 | S>C | A:267 | (2.41, -12.81, 1.20) | |
| 3:33093480 | rs371546950 | Y>C | A:270 | (-3.28, -14.40, 7.68) |
| 3:33093481 | rs376663785 CM012603 |
Y>D | A:270 | (-3.28, -14.40, 7.68) |
| 3:33093471 | rs72555362 | W>L | A:273 | (-7.23, -11.81, 12.12) |
| 3:33093472 | W>R | A:273 | (-7.23, -11.81, 12.12) | |
| 3:33093448 | H>Y | A:281 | (-7.17, -12.67, 22.14) | |
| 3:33093439 | I>V | A:284 | (-5.50, -19.43, 15.28) | |
| 3:33093430 | COSM161272 | E>K | A:287 | (-2.23, -28.71, 14.34) |
| 3:33093427 | A>T | A:288 | (-3.77, -25.14, 12.03) | |
| 3:33093414 | rs368139032 | S>C | A:292 | (-1.53, -25.14, 6.59) |
| 3:33093405 | rs76016860 | D>G | A:295 | (-0.09, -28.47, 3.16) |
| 3:33093387 | A>V | A:301 | (5.65, -22.36, -1.86) | |
| 3:33093286 | M>V | A:307 | (2.57, -11.29, 12.37) | |
| 3:33093274 | rs368568171 | G>R | A:311 | (3.71, -6.57, 19.35) |
| 3:33093267 | N>S | A:313 | (0.21, -0.72, 18.82) | |
| 3:33087686 | D>N | A:332 | (0.26, -10.97, 20.66) | |
| 3:33087682 | rs370107958 CM090781 |
Y>C | A:333 | (-1.99, -11.38, 14.86) |
| 3:33087670 | L>P | A:337 | (7.30, -14.69, 18.71) | |
| 3:33087650 | T>A | A:344 | (5.29, -20.07, 21.79) | |
| 3:33087642 | K>N | A:346 | (2.17, -21.20, 17.47) | |
| 3:33087628 | R>Q | A:351 | (12.29, -25.44, 14.97) | |
| 3:33065815 | F>L | A:357 | (9.95, -29.02, 4.17) | |
| 3:33065793 | I>V | A:365 | (16.77, -20.74, 20.84) | |
| 3:33065790 | P>A | A:366 | (17.44, -16.95, 21.95) | |
| 3:33065775 | K>Q | A:371 | (9.16, -11.31, 32.40) | |
| 3:33063122 | D>G | A:390 | (-1.24, 27.14, 30.18) | |
| 3:33063116 | L>R | A:392 | (-1.09, 20.78, 27.18) | |
| 3:33063111 | P>S | A:394 | (2.07, 26.58, 24.60) | |
| 3:33063099 | rs199692082 | I>V | A:398 | (-7.96, 28.01, 17.03) |
| 3:33063077 | T>K | A:405 | (-10.82, 19.08, 12.32) | |
| 3:33063063 | K>Q | A:410 | (-2.22, 21.89, 12.08) | |
| 3:33060031 | R>Q | A:419 | (-13.08, 25.84, 26.49) | |
| 3:33060032 | R>W | A:419 | (-13.08, 25.84, 26.49) | |
| 3:33060029 | rs200181401 CM064032 |
T>P | A:420 | (-18.16, 26.87, 24.50) |
| 3:33060026 | T>A | A:421 | (-20.45, 29.55, 26.41) | |
| 3:33060022 | L>R | A:422 | (-23.69, 27.23, 28.25) | |
| 3:33060014 | D>H | A:425 | (-30.30, 28.05, 32.14) | |
| 3:33060011 | C>G | A:426 | (-28.97, 24.30, 31.68) | |
| 3:33060004 | N>S | A:428 | (-33.75, 21.88, 33.81) | |
| 3:33060001 | rs201148460 | P>L | A:429 | (-31.65, 18.58, 32.10) |
| 3:33060002 | rs180869784 | P>S | A:429 | (-31.65, 18.58, 32.10) |
| 3:33059981 | rs34421970 | L>F | A:436 | (-24.60, 14.50, 11.40) |
| 3:33059966 | COSM1208253 CM064028 |
D>N | A:441 | (-13.57, 8.75, 17.95) |
| 3:33059962 | rs564428355 CM057874 |
R>Q | A:442 | (-14.93, 8.18, 23.80) |
| 3:33059944 | D>V | A:448 | (-18.34, 25.12, 35.15) | |
| 3:33059945 | D>N | A:448 | (-18.34, 25.12, 35.15) | |
| 3:33058304 | N>S | A:459 | (-22.52, 4.03, 20.44) | |
| 3:33058287 | I>V | A:465 | (-25.75, 19.19, 29.78) | |
| 3:33058257 | L>F | A:475 | (-15.95, 18.76, 24.51) | |
| 3:33058250 | rs374547468 | V>A | A:477 | (-11.85, 14.96, 21.57) |
| 3:33058238 | G>E | A:481 | (-8.04, 5.79, 15.41) | |
| 3:33058239 | G>R | A:481 | (-8.04, 5.79, 15.41) | |
| 3:33058235 | rs72555391 | R>H | A:482 | (-6.68, 8.54, 11.91) |
| 3:33058224 | G>S | A:486 | (-11.46, 0.95, 3.48) | |
| 3:33058217 | Y>C | A:488 | (-15.59, 4.76, 4.88) | |
| 3:33058209 | COSM3592499 COSM3592498 CM990699 CM070943 |
D>N | A:491 | (-10.77, 9.25, 9.92) |
| 3:33055801 | rs202007119 CM106678 |
G>V | A:494 | (-13.15, 15.23, 16.10) |
| 3:33055784 | rs72555368 | T>A | A:500 | (-26.82, 20.70, 19.23) |
| 3:33055781 | L>V | A:501 | (-27.70, 22.94, 23.47) | |
| 3:33055778 | S>G | A:502 | (-31.71, 22.38, 22.79) | |
| 3:33055771 | rs372538696 | N>S | A:504 | (-30.09, 25.36, 19.06) |
| 3:33055762 | rs369598326 | T>M | A:507 | (-21.54, 29.18, 18.15) |
| 3:33055753 | rs1803198 | T>M | A:510 | (-11.89, 28.00, 22.18) |
| 3:33055749 | rs375113962 | I>M | A:511 | (-10.02, 24.80, 19.49) |
| 3:33055738 | D>G | A:515 | (1.37, 19.67, 23.33) | |
| 3:33055732 | E>G | A:517 | (3.48, 13.38, 24.41) | |
| 3:33055720 | rs186781398 | C>Y | A:521 | (8.59, 14.57, 27.05) |
| 3:33055721 | rs4302331 | C>R | A:521 | (8.59, 14.57, 27.05) |
| 3:33055709 | rs368610739 | G>R | A:525 | (6.73, 21.99, 34.03) |
| 3:33055705 | rs147332381 | G>D | A:526 | (8.41, 20.95, 36.71) |
| 3:33055694 | rs371397760 | R>C | A:530 | (17.87, 23.37, 30.86) |
| 3:33055648 | N>S | A:545 | (-19.67, 8.33, 38.47) | |
| 3:33055642 | rs200062755 | T>M | A:547 | (-13.42, 11.75, 37.12) |
| 3:33055643 | T>P | A:547 | (-13.42, 11.75, 37.12) | |
| 3:33055640 | L>F | A:548 | (-12.36, 16.02, 35.69) | |
| 3:33055636 | P>L | A:549 | (-10.12, 14.61, 32.67) | |
| 3:33055595 | P>A | A:563 | (22.90, -8.26, 37.29) | |
| 3:33055587 | L>F | A:565 | (17.12, -5.67, 37.97) | |
| 3:33055567 | rs183126947 | Q>R | A:572 | (-2.41, -4.65, 36.13) |
| 3:33055549 | rs371582179 CM930343 |
K>R | A:578 | (-10.16, 5.15, 28.58) |
| 3:33055550 | K>E | A:578 | (-10.16, 5.15, 28.58) | |
| 3:33038835 | G>D | A:579 | (-6.21, 5.68, 28.94) | |
| 3:33038802 | rs398123351 CM930344 |
R>H | A:590 | (-4.68, 4.00, 23.39) |
| 3:33038799 | rs72555371 | Y>C | A:591 | (-5.67, 2.92, 30.54) |
| 3:33038800 | rs72555373 CM000716 |
Y>H | A:591 | (-5.67, 2.92, 30.54) |
| 3:33038787 | rs199694629 COSM1043687 COSM1651374 |
R>Q | A:595 | (-14.65, -2.34, 25.96) |
| 3:33038788 | rs201807974 CM073106 |
R>W | A:595 | (-14.65, -2.34, 25.96) |
| 3:33038778 | Q>R | A:598 | (-5.16, -5.13, 26.59) | |
| 3:33038757 | Q>L | A:605 | (14.64, -3.52, 30.24) | |
| 3:33038742 | T>N | A:610 | (18.86, 2.13, 38.06) | |
| 3:33038727 | rs139542437 | T>N | A:615 | (7.96, 8.77, 36.44) |
| 3:33038698 | P>T | A:625 | (-8.96, 4.96, 41.63) | |
| 3:33038692 | S>R | A:627 | (-11.50, 10.01, 45.60) | |
| 3:33038688 | rs568274819 | S>N | A:628 | (-10.84, 7.62, 48.72) |
| 3:33038682 | D>G | A:630 | (-7.56, 4.22, 50.43) | |
| 3:33038667 | A>V | A:635 | (-2.72, 2.37, 41.99) | |
| 3:33038661 | rs369133124 | T>M | A:637 | (0.11, -3.35, 39.56) |
| 3:33038640 | I>T | A:644 | (-3.90, -10.32, 26.17) |
[+] ClinVar Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 3:33114136 | rs72555358 | R>C | A:49 | (11.06, -22.38, -0.71) |
| 3:33114129 | rs72555390 | I>T | A:51 | (10.50, -19.90, 4.75) |
| 3:33114105 | rs72555392 | R>H | A:59 | (3.83, -2.96, 15.55) |
| 3:33114078 | rs572237881 | R>Q | A:68 | (12.32, -9.92, 19.39) |
| 3:33114079 | rs72555370 | R>W | A:68 | (12.32, -9.92, 19.39) |
| 3:33114036 | rs72555393 | T>M | A:82 | (8.65, -5.14, 6.86) |
| 3:33110461 | rs72555364 | Y>D | A:83 | (3.85, -3.53, 6.28) |
| 3:33110383 | rs35289681 | R>W | A:109 | (22.15, -2.13, 8.07) |
| 3:33110341 | rs28934274 | G>R | A:123 | (3.59, 0.97, -0.09) |
| 3:33109737 | rs192732174 | R>C | A:148 | (-5.47, 3.35, -1.58) |
| 3:33099712 | rs189115557 | R>H | A:201 | (-0.35, 2.28, -14.69) |
| 3:33099713 | rs72555360 | R>C | A:201 | (-0.35, 2.28, -14.69) |
| 3:33099692 | rs72555366 | R>C | A:208 | (11.29, -0.67, -11.67) |
| 3:33093480 | rs371546950 | Y>C | A:270 | (-3.28, -14.40, 7.68) |
| 3:33093471 | rs72555362 | W>L | A:273 | (-7.23, -11.81, 12.12) |
| 3:33093388 | rs727503954 | A>T | A:301 | (5.65, -22.36, -1.86) |
| 3:33093283 | rs587779404 | F>L | A:308 | (7.13, -15.37, 13.61) |
| 3:33093258 | rs72555361 | Y>C | A:316 | (-1.34, 8.18, 20.59) |
| 3:33087676 | rs398123347 | A>V | A:335 | (2.05, -15.08, 17.49) |
| 3:33065789 | rs797045010 | P>H | A:366 | (17.44, -16.95, 21.95) |
| 3:33063068 | rs72555369 | Q>P | A:408 | (-8.97, 22.22, 10.38) |
| 3:33060002 | rs180869784 | P>S | A:429 | (-31.65, 18.58, 32.10) |
| 3:33059981 | rs34421970 | L>F | A:436 | (-24.60, 14.50, 11.40) |
| 3:33059977 | rs202237232 | N>I | A:437 | (-22.23, 10.47, 14.31) |
| 3:33059974 | rs72555367 | G>E | A:438 | (-19.23, 13.87, 15.02) |
| 3:33058310 | rs28934886 | R>Q | A:457 | (-17.27, 7.24, 15.58) |
| 3:33058235 | rs72555391 | R>H | A:482 | (-6.68, 8.54, 11.91) |
| 3:33058236 | rs72555365 | R>C | A:482 | (-6.68, 8.54, 11.91) |
| 3:33055784 | rs72555368 | T>A | A:500 | (-26.82, 20.70, 19.23) |
| 3:33055755 | rs72555363 | W>C | A:509 | (-16.79, 25.80, 19.80) |
| 3:33038802 | rs398123351 | R>H | A:590 | (-4.68, 4.00, 23.39) |
| 3:33038803 | rs794727165 | R>C | A:590 | (-4.68, 4.00, 23.39) |
| 3:33038799 | rs72555371 | Y>C | A:591 | (-5.67, 2.92, 30.54) |
| 3:33038800 | rs72555373 | Y>N | A:591 | (-5.67, 2.92, 30.54) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 3:33114174 | COSM480030 | Y>C | A:36 | (8.52, -15.92, -14.99) |
| 3:33114127 | COSM2984273 | S>A | A:52 | (8.93, -15.41, 5.86) |
| 3:33099680 | COSM3660489 | G>R | A:212 | (15.26, -0.39, -10.83) |
| 3:33099620 | COSM4411163 | A>T | A:232 | (-3.37, -6.67, -10.62) |
| 3:33093430 | COSM161272 | E>K | A:287 | (-2.23, -28.71, 14.34) |
| 3:33038745 | COSM1422425 | M>T | A:609 | (16.11, 4.53, 35.53) |