1W6J.A | LSS – ASTRID

1W6J.A | LSS

General Structure Information

PDB ID	1w6j
HGNC Gene Label(s)	LSS
Structure Name	structure of human osc in complex with ro 48-8071
Resolution	2.2Å
Reference	AUTH R.THOMA,T.SCHULZ-GASCH,B.DARCY,J.BENZ,J.AEBI,AUTH 2 H.DEHMLOW,M.HENNIG,M.STIHLE,A.RUFTITL INSIGHT INTO STEROID SCAFFOLD FORMATION FROM THETITL 2 STRUCTURE OF HUMAN OXIDOSQUALENE CYCLASEREF NATURE V. 432 118 2004REFN ISSN 0028-0836PMID 15525992DOI 10.1038/NATURE02993

Variant Set Distributions

ExAC Variants

Number Of Residues	727
Number Of SNVs	216
Number Of Permutations	70157
Optimal Distance Threshold	11.0
K Statistic	0.033
p-value	0.059

COSMIC

Number Of Residues	727
Number Of SNVs	10
Number Of Permutations	2725
Optimal Distance Threshold	27.0
K Statistic	0.178
p-value	0.046

Ripley’s K Analysis Plots

ExACCOSMIC

Variant Set Comparisons

Cosmic vs. ExAC

Number Of ExAC SNVs	216
Number Of COSMIC SNVs	10
Optimal Distance Threshold	27.0
K Statistic	-0.147
p-value	0.182

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
21:47648502	COSM1534858	R>L	A:9	(46.38, 77.46, -5.28)
21:47648500		R>G	A:10	(46.58, 70.37, -4.34)
21:47648497		G>R	A:11	(48.43, 73.91, 0.59)
21:47648481		T>N	A:16	(50.07, 86.66, 0.89)
21:47648476		P>S	A:18	(49.92, 92.37, 3.29)
21:47648458		R>C	A:24	(48.25, 98.66, 14.00)
21:47648449		L>F	A:27	(42.58, 87.29, 18.53)
21:47648445	rs369422998	N>S	A:28	(40.06, 89.45, 21.13)
21:47648438	rs565392079 COSM579372	E>D	A:30	(34.62, 86.18, 25.97)
21:47648436	rs199791898	R>K	A:31	(32.41, 81.91, 27.88)
21:47648434		G>S	A:32	(35.51, 81.09, 22.22)
21:47648426		Q>H	A:34	(37.42, 83.13, 17.54)
21:47648413		L>V	A:39	(44.81, 98.38, 16.69)
21:47648409		Q>L	A:40	(43.14, 102.64, 13.96)
21:47648389		E>K	A:47	(52.86, 93.77, 23.42)
21:47648379		G>V	A:50	(52.27, 84.72, 19.17)
21:47648350		T>A	A:60	(57.36, 83.33, 15.58)
21:47647591	rs142908964	K>M	A:65	(62.75, 78.57, 22.13)
21:47647583		P>S	A:68	(66.08, 70.37, 21.05)
21:47647577		A>T	A:70	(63.98, 64.96, 17.51)
21:47647573		H>R	A:71	(66.79, 62.27, 16.96)
21:47647568	rs572447104 COSM1031581	A>T	A:73	(58.84, 59.84, 20.00)
21:47647553		L>V	A:78	(58.18, 67.29, 24.64)
21:47647548		N>K	A:79	(59.52, 69.33, 20.84)
21:47647546	rs371394924	G>E	A:80	(54.97, 69.74, 20.23)
21:47647542		M>I	A:81	(53.46, 69.04, 23.91)
21:47647534		Y>F	A:84	(49.01, 73.13, 20.07)
21:47647532	rs377388671	V>M	A:85	(50.97, 74.81, 24.91)
21:47647510		G>E	A:92	(41.71, 77.41, 26.86)
21:47647486	rs536205721	G>V	A:100	(37.92, 76.85, 2.13)
21:47647483		P>L	A:101	(35.00, 77.05, 1.90)
21:47647469		P>S	A:106	(29.88, 85.53, -1.43)
21:47647466		G>C	A:107	(26.69, 86.19, 0.88)
21:47642632	rs369815137 COSM3785483	V>M	A:114	(21.01, 94.55, 0.41)
21:47642628		A>V	A:115	(21.73, 95.99, 4.33)
21:47642626	rs139003098	R>C	A:116	(23.33, 100.51, 2.93)
21:47642590		V>M	A:128	(40.15, 92.21, -1.27)
21:47642586	rs200708561 COSM189566	R>Q	A:129	(45.29, 89.62, 1.55)
21:47642578	rs150430075	R>W	A:132	(43.09, 90.42, -5.43)
21:47642572	rs373432079	V>L	A:134	(42.47, 82.32, -3.46)
21:47642556		G>D	A:139	(41.02, 83.54, -12.88)
21:47641884		I>T	A:145	(41.16, 76.22, -1.23)
21:47641885		I>V	A:145	(41.16, 76.22, -1.23)
21:47641878		D>A	A:147	(38.36, 73.24, -6.96)
21:47641867		V>M	A:151	(30.51, 79.21, -12.80)
21:47641854		A>V	A:155	(30.70, 84.60, -10.24)
21:47641845		Y>C	A:158	(33.40, 89.75, -11.07)
21:47641829		I>M	A:163	(30.21, 94.38, -3.63)
21:47641816		P>S	A:168	(35.40, 96.54, -14.16)
21:47641810	rs140196762	D>N	A:170	(41.07, 94.95, -11.88)
21:47641794	rs2839158	R>Q	A:175	(42.67, 87.05, -14.85)
21:47641788	rs142081800	R>Q	A:177	(35.03, 89.88, -17.16)
21:47641789		R>W	A:177	(35.03, 89.88, -17.16)
21:47641777	rs189748455	H>N	A:181	(32.08, 85.34, -20.25)
21:47639478	rs149739328	V>M	A:187	(23.22, 81.32, -17.35)
21:47639468		P>R	A:190	(25.05, 76.60, -9.60)
21:47639449	rs143911342	W>C	A:196	(23.23, 84.61, -2.23)
21:47639430	COSM1726603	Y>H	A:203	(19.64, 84.68, -12.30)
21:47639427		S>G	A:204	(15.57, 85.90, -12.52)
21:47639411		N>S	A:209	(14.07, 75.38, -9.88)
21:47639408		T>I	A:210	(10.52, 76.22, -6.75)
21:47639392	rs111335500	M>I	A:215	(7.93, 71.85, 1.91)
21:47639391		W>R	A:216	(9.31, 74.31, 6.24)
21:47636418	rs147410319	P>L	A:223	(6.70, 62.64, 2.50)
21:47636400	rs369733014	L>H	A:229	(15.37, 66.98, 6.05)
21:47636392		H>Y	A:232	(23.90, 72.01, 8.22)
21:47636386	rs538836283	R>W	A:234	(16.38, 71.70, 8.76)
21:47636359		C>G	A:243	(13.94, 85.17, 0.14)
21:47636353	rs553607050	A>T	A:245	(8.50, 84.17, -1.35)
21:47636350	rs150614553	V>I	A:246	(9.43, 87.82, -0.66)
21:47636346		R>Q	A:247	(10.16, 86.48, -5.65)
21:47636334	rs61735801	A>V	A:251	(17.89, 97.99, -5.62)
21:47636335	rs372457825	A>T	A:251	(17.89, 97.99, -5.62)
21:47636330		E>D	A:252	(17.62, 98.56, -10.47)
21:47636328	rs567962408	D>G	A:253	(22.43, 99.94, -7.77)
21:47636325		P>L	A:254	(24.60, 101.75, -10.40)
21:47636307	rs570157673 COSM1031576	R>H	A:260	(21.55, 93.50, -14.70)
21:47635689		F>V	A:268	(20.06, 90.94, -18.57)
21:47635685		A>V	A:269	(17.16, 91.46, -22.12)
21:47635686	rs143692945	A>T	A:269	(17.16, 91.46, -22.12)
21:47635679		I>T	A:271	(18.20, 86.08, -20.80)
21:47635673		W>L	A:273	(16.39, 84.67, -16.92)
21:47635655		N>S	A:279	(21.89, 75.87, -17.18)
21:47635644		D>N	A:283	(32.49, 70.52, -16.00)
21:47635641	COSM1732412	E>K	A:284	(30.29, 73.07, -11.62)
21:47635635		Y>H	A:286	(29.36, 65.10, -6.90)
21:47635631	rs79710966	T>M	A:287	(24.43, 65.76, -7.74)
21:47635628		P>L	A:288	(23.01, 64.93, -11.21)
21:47635610	rs188459967	R>H	A:294	(14.90, 66.70, -13.83)
21:47635611		R>C	A:294	(14.90, 66.70, -13.83)
21:47635608		V>M	A:295	(8.99, 64.73, -12.14)
21:47635605		V>I	A:296	(9.11, 66.95, -8.36)
21:47635601		Y>C	A:297	(12.07, 71.00, -8.88)
21:47635197	rs150061696	Y>C	A:303	(1.50, 75.50, -6.68)
21:47635191	rs375558460	H>P	A:305	(2.37, 80.35, -13.00)
21:47635181		S>R	A:308	(-2.15, 79.97, -2.98)
21:47635176	rs34115287	H>R	A:310	(-4.27, 81.82, 2.23)
21:47635170		R>Q	A:312	(3.57, 81.48, -1.05)
21:47635164		R>Q	A:314	(-0.55, 79.03, 6.37)
21:47635159	rs371221726	V>M	A:316	(5.93, 83.44, 4.81)
21:47635137	rs576764305	I>T	A:323	(14.13, 82.40, 10.90)
21:47635138	rs544052419	I>V	A:323	(14.13, 82.40, 10.90)
21:47635129		D>N	A:326	(18.09, 79.79, 14.77)
21:47635119	rs367696830	F>S	A:329	(16.89, 78.56, 20.08)
21:47635114		K>Q	A:331	(23.09, 84.32, 21.45)
21:47635095	rs139587765	P>R	A:337	(27.88, 80.50, 7.69)
21:47633736		I>S	A:342	(20.04, 83.93, 4.49)
21:47633733		N>S	A:343	(18.71, 84.21, 9.09)
21:47633734		N>D	A:343	(18.71, 84.21, 9.09)
21:47633721	rs144462108	R>H	A:347	(15.23, 89.22, 11.78)
21:47633722		R>C	A:347	(15.23, 89.22, 11.78)
21:47633717		W>C	A:348	(17.00, 94.68, 5.64)
21:47633706		G>E	A:352	(14.90, 96.13, 10.51)
21:47633707	rs373046759	G>R	A:352	(14.90, 96.13, 10.51)
21:47633701	rs369138798 COSM1214056	A>T	A:354	(16.58, 99.49, 14.06)
21:47633698		S>T	A:355	(16.26, 95.91, 14.89)
21:47633671		R>G	A:364	(27.54, 87.16, 17.10)
21:47633664	rs190225473	P>L	A:366	(32.78, 89.39, 13.57)
21:47632965		M>L	A:371	(43.19, 87.53, 9.70)
21:47632961		G>D	A:372	(45.08, 84.74, 7.71)
21:47632947	rs140511660	K>E	A:377	(39.36, 83.42, 5.67)
21:47630651		N>S	A:382	(31.52, 79.83, 15.29)
21:47630649		G>S	A:383	(34.51, 77.36, 14.74)
21:47630635		W>C	A:387	(36.51, 68.31, 16.75)
21:47630631		T>A	A:389	(40.08, 71.72, 22.92)
21:47630628		A>T	A:390	(39.07, 67.77, 22.92)
21:47630622		A>T	A:392	(44.26, 68.36, 22.54)
21:47630619	rs138129293	I>F	A:393	(42.76, 67.29, 26.19)
21:47629538		A>V	A:399	(52.15, 62.31, 25.57)
21:47629522		R>S	A:404	(56.52, 67.49, 31.48)
21:47629518	rs530087387	E>K	A:406	(55.80, 72.30, 31.74)
21:47629511		S>L	A:408	(49.51, 72.16, 34.56)
21:47629508		S>C	A:409	(48.01, 75.74, 33.46)
21:47629470		Q>E	A:422	(28.33, 71.25, 29.33)
21:47628190	rs566634216	Q>R	A:431	(10.17, 69.33, 20.87)
21:47628169	rs138907803	R>H	A:438	(20.81, 72.04, 24.03)
21:47628170	rs142026899	R>G	A:438	(20.81, 72.04, 24.03)
21:47627472		T>M	A:446	(30.72, 77.93, 20.76)
21:47627461	rs375698498 COSM1414589	G>S	A:450	(24.22, 75.06, 20.65)
21:47627439		T>M	A:457	(29.28, 65.13, 23.12)
21:47627430		A>G	A:460	(34.26, 66.18, 25.52)
21:47627431	rs368794734	A>T	A:460	(34.26, 66.18, 25.52)
21:47627426		L>F	A:461	(32.46, 62.87, 27.94)
21:47627422		A>T	A:463	(38.37, 64.60, 27.84)
21:47627395		P>S	A:472	(45.57, 65.98, 40.43)
21:47627390		H>Q	A:473	(46.97, 69.82, 40.80)
21:47627376		I>N	A:478	(32.16, 68.26, 35.16)
21:47627368	rs141324417	E>K	A:481	(24.56, 66.26, 37.67)
21:47627364		R>Q	A:482	(27.20, 68.97, 34.71)
21:47627365		R>W	A:482	(27.20, 68.97, 34.71)
21:47627355		D>G	A:485	(23.15, 65.33, 31.47)
21:47627356	COSM419664	D>N	A:485	(23.15, 65.33, 31.47)
21:47626660		D>G	A:497	(21.57, 51.53, 12.07)
21:47626654		G>V	A:499	(24.18, 54.32, 14.59)
21:47626642		Y>C	A:503	(24.41, 68.49, 14.27)
21:47626630	rs199896537 COSM288754	R>H	A:507	(14.78, 63.35, 12.14)
21:47626628	rs377016169	G>W	A:508	(14.83, 59.50, 7.12)
21:47626624	rs538487837	G>V	A:509	(15.02, 58.13, 4.07)
21:47626616	rs113709086	L>M	A:512	(14.62, 61.59, 0.93)
21:47626607		L>V	A:515	(14.60, 64.91, -3.56)
21:47626597		S>L	A:518	(22.64, 71.15, -4.50)
21:47626586	rs149012686	G>R	A:522	(26.55, 65.15, -1.17)
21:47625849		I>T	A:524	(22.31, 67.01, 1.53)
21:47625811	COSM1682076	V>M	A:537	(29.68, 57.36, 20.83)
21:47625808		M>V	A:538	(31.43, 52.96, 20.72)
21:47625801	rs373861822	A>V	A:540	(32.70, 57.47, 25.39)
21:47625759		A>V	A:554	(21.86, 47.98, 29.59)
21:47625750		R>Q	A:557	(26.52, 46.40, 28.83)
21:47625751		R>W	A:557	(26.52, 46.40, 28.83)
21:47616170		T>M	A:561	(26.68, 45.40, 20.69)
21:47616164		G>V	A:563	(27.84, 49.52, 16.93)
21:47616159		E>Q	A:565	(27.51, 44.62, 14.32)
21:47616156		F>L	A:566	(26.96, 50.98, 11.67)
21:47616150	COSM4102199	R>G	A:568	(31.05, 43.84, 11.77)
21:47616147		R>W	A:569	(26.15, 45.41, 8.98)
21:47616132		D>N	A:574	(38.86, 46.94, 0.88)
21:47615668		S>C	A:580	(32.53, 61.71, 5.63)
21:47615647		Y>C	A:587	(38.96, 60.50, 9.50)
21:47615644		G>D	A:588	(37.77, 55.90, 8.73)
21:47615645	rs561449819 COSM1256977	G>S	A:588	(37.77, 55.90, 8.73)
21:47615642		T>A	A:589	(40.08, 52.98, 8.67)
21:47615632	rs543025517	G>D	A:592	(37.13, 51.45, 13.07)
21:47615629		L>P	A:593	(40.69, 50.00, 13.55)
21:47615621		F>L	A:596	(36.30, 46.32, 15.62)
21:47615614		C>Y	A:598	(36.75, 49.52, 22.33)
21:47615610	rs140469889	M>I	A:599	(34.29, 46.27, 21.76)
21:47615593	rs528126813	D>V	A:605	(48.77, 35.04, 19.42)
21:47615590		G>A	A:606	(49.18, 37.27, 15.05)
21:47614571	rs374703920	A>T	A:608	(42.80, 38.89, 13.84)
21:47614555	rs541033155	S>F	A:613	(43.04, 41.70, 9.20)
21:47614552		R>Q	A:614	(39.40, 42.69, 5.56)
21:47614553	rs35785446	R>W	A:614	(39.40, 42.69, 5.56)
21:47614531	rs367866911	S>F	A:621	(49.36, 48.17, 0.99)
21:47614528	rs61735802	R>Q	A:622	(47.18, 51.54, 0.22)
21:47614520		A>T	A:625	(58.74, 55.14, 0.73)
21:47614506		W>C	A:629	(50.41, 55.83, 5.52)
21:47614504	rs534377438	G>V	A:630	(48.48, 59.72, 1.15)
21:47614489	rs567412173	S>F	A:635	(39.47, 60.40, -2.37)
21:47614486		C>F	A:636	(36.20, 62.24, -1.24)
21:47614484		E>K	A:637	(35.55, 64.21, -5.38)
21:47614480		E>G	A:638	(35.93, 59.98, -7.40)
21:47614477		R>Q	A:639	(32.46, 57.15, -2.83)
21:47614474		R>H	A:640	(38.84, 56.22, -6.28)
21:47614475	rs148491294	R>C	A:640	(38.84, 56.22, -6.28)
21:47614469	rs2254524	L>V	A:642	(42.91, 59.13, -4.89)
21:47614464		Q>H	A:643	(48.52, 58.09, -3.47)
21:47614460		A>T	A:645	(52.67, 62.87, -4.25)
21:47614442		N>D	A:651	(46.74, 60.79, 5.96)
21:47614422	COSM3799994	M>I	A:657	(46.46, 56.33, 15.69)
21:47614409		V>I	A:662	(44.67, 46.73, 16.61)
21:47614405		R>Q	A:663	(47.79, 46.98, 20.27)
21:47611860		E>K	A:668	(59.97, 47.25, 11.64)
21:47611838	rs549479604	R>Q	A:675	(62.08, 56.58, 11.69)
21:47611839	rs538130640	R>W	A:675	(62.08, 56.58, 11.69)
21:47611818		L>F	A:682	(59.50, 72.67, 12.13)
21:47611811		N>S	A:684	(59.32, 75.59, 16.43)
21:47611812		N>H	A:684	(59.32, 75.59, 16.43)
21:47611796		Q>P	A:689	(50.06, 73.98, 5.96)
21:47611146		N>D	A:691	(47.55, 69.02, 1.21)
21:47611115		A>G	A:701	(37.05, 71.50, 1.50)
21:47611113		I>V	A:702	(37.19, 72.44, 5.66)
21:47611103		T>M	A:705	(44.72, 74.33, 11.61)
21:47611104		T>A	A:705	(44.72, 74.33, 11.61)
21:47611100		S>N	A:706	(45.24, 71.82, 14.88)
21:47611097	rs566088146	Y>C	A:707	(43.37, 67.79, 12.44)
21:47611095		R>G	A:708	(49.36, 71.63, 11.23)
21:47611076		W>L	A:714	(46.08, 61.35, 19.78)
21:47611073	rs377110619	A>V	A:715	(51.08, 59.23, 17.47)
21:47611065	rs150463602	R>C	A:718	(48.71, 55.75, 20.58)
21:47611047		P>S	A:724	(58.68, 51.22, 26.28)
21:47611044		E>Q	A:725	(60.77, 48.27, 24.37)
21:47611040		R>T	A:726	(61.33, 49.14, 20.00)
21:47611038		A>T	A:727	(64.98, 53.24, 20.89)
21:47611035		L>F	A:728	(62.30, 55.28, 17.86)
21:47611032		A>P	A:729	(60.57, 55.69, 21.95)
21:47611023		P>T	A:732	(58.59, 56.59, 27.20)

1W6J.A | LSS.

1W6J.A | LSS

General Structure Information

Variant Set Distributions

Ripley’s K Analysis Plots

Variant Set Comparisons

Mapped Variants

[+] ExAC Missense Variants

[+] COSMIC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
21:47648371	COSM1751698	A>T	A:53	(51.98, 86.02, 14.79)
21:47647529	COSM251029	G>W	A:86	(51.51, 78.46, 22.99)
21:47641794	COSM4135100	R>Q	A:175	(42.67, 87.05, -14.85)
21:47636346	COSM2889936	R>Q	A:247	(10.16, 86.48, -5.65)
21:47635176	COSM444623	H>R	A:310	(-4.27, 81.82, 2.23)
21:47627403	COSM2889924	E>A	A:469	(41.50, 58.77, 35.53)
21:47626625	COSM3379211	G>R	A:509	(15.02, 58.13, 4.07)
21:47615617	COSM224085	A>V	A:597	(39.57, 48.12, 20.06)
21:47614469	COSM444622	L>V	A:642	(42.91, 59.13, -4.89)
21:47611140	COSM3964037	A>S	A:693	(41.99, 67.45, 6.03)