3E6U.A | LANCL1

General Structure Information

PDB ID	3e6u
HGNC Gene Label(s)	LANCL1
Structure Name	crystal structure of human lancl1
Resolution	2.6Å
Reference	AUTH W.ZHANG,L.WANG,Y.LIU,J.XU,G.ZHU,H.CANG,X.LI,AUTH 2 M.BARTLAM,K.HENSLEY,G.LI,Z.RAO,X.C.ZHANGTITL STRUCTURE OF HUMAN LANTHIONINE SYNTHETASE C-LIKETITL 2 PROTEIN 1 AND ITS INTERACTION WITH EPS8 ANDTITL 3 GLUTATHIONEREF GENES DEV. V. 23 1387 2009REFN ISSN 0890-9369PMID 19528316DOI 10.1101/GAD.1789209

Variant Set Distributions

ExAC Variants

Number Of Residues	399
Number Of SNVs	132
Number Of Permutations	47668
Optimal Distance Threshold	10.0
K Statistic	0.046
p-value	0.352

COSMIC

Number Of Residues	399
Number Of SNVs	4
Number Of Permutations	1529
Optimal Distance Threshold	26.0
K Statistic	0.167
p-value	0.368

Ripley’s K Analysis Plots

ExACCOSMIC

Variant Set Comparisons

Cosmic vs. ExAC

Number Of ExAC SNVs	132
Number Of COSMIC SNVs	3
Optimal Distance Threshold	26.0
K Statistic	-0.464
p-value	0.262

Pathogenic Proximity Analysis

COSMIC PathProx Analysis

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
2:211341107		A>G	A:5	(16.54, 165.20, 196.57)
2:211341096		P>S	A:9	(25.67, 158.51, 196.30)
2:211341092	rs370376380	Y>C	A:10	(25.65, 156.44, 193.22)
2:211341089		A>V	A:11	(30.70, 158.18, 191.53)
2:211341086		D>V	A:12	(30.81, 160.61, 187.78)
2:211341083	COSM3783397	Y>F	A:13	(32.68, 157.65, 183.09)
2:211341080		N>S	A:14	(35.85, 156.18, 185.89)
2:211341081	rs201205857	N>H	A:14	(35.85, 156.18, 185.89)
2:211341066		E>K	A:19	(35.61, 147.96, 183.75)
2:211341056		F>C	A:22	(29.62, 149.66, 180.56)
2:211341054		D>H	A:23	(31.68, 146.15, 177.32)
2:211336799		L>P	A:28	(25.10, 145.43, 180.37)
2:211336793		P>R	A:30	(26.84, 139.36, 182.60)
2:211336794		P>S	A:30	(26.84, 139.36, 182.60)
2:211336789		E>D	A:31	(27.16, 140.73, 187.68)
2:211336790		E>V	A:31	(27.16, 140.73, 187.68)
2:211336791		E>K	A:31	(27.16, 140.73, 187.68)
2:211336778	rs541123400	R>H	A:35	(22.46, 143.08, 190.37)
2:211336779		R>C	A:35	(22.46, 143.08, 190.37)
2:211336769		N>S	A:38	(17.33, 138.46, 189.65)
2:211336765	rs369638285 COSM3962293	K>N	A:39	(14.94, 143.45, 191.72)
2:211336766	rs145822948	K>R	A:39	(14.94, 143.45, 191.72)
2:211336760		R>Q	A:41	(12.81, 136.91, 187.27)
2:211336743		M>V	A:47	(3.10, 143.75, 189.93)
2:211336713	rs142719586	R>W	A:57	(-14.16, 149.83, 186.15)
2:211336703		T>S	A:60	(-5.64, 153.83, 181.93)
2:211336704		T>A	A:60	(-5.64, 153.83, 181.93)
2:211336701	rs139516654	G>S	A:61	(-1.97, 153.62, 181.24)
2:211336698		Y>H	A:62	(-0.87, 157.97, 184.06)
2:211320033		A>S	A:69	(0.05, 145.51, 178.94)
2:211320030		V>L	A:70	(2.50, 148.27, 177.79)
2:211320008		D>A	A:77	(9.86, 141.89, 173.02)
2:211320002	rs372346977	F>S	A:79	(13.12, 138.72, 179.33)
2:211319993		P>L	A:82	(5.72, 132.69, 176.71)
2:211319991		A>T	A:83	(3.86, 134.22, 180.00)
2:211319988	rs199718830	Y>H	A:84	(6.35, 137.72, 180.63)
2:211319981		Q>R	A:86	(-0.83, 134.69, 177.64)
2:211319972		H>R	A:89	(-4.88, 138.21, 176.24)
2:211319963		V>E	A:92	(-5.92, 143.83, 176.97)
2:211319961	rs369885403	K>Q	A:93	(-9.34, 140.35, 178.10)
2:211319957		Q>R	A:94	(-9.01, 143.59, 182.78)
2:211319942	rs551069033	L>S	A:99	(-13.87, 151.71, 176.91)
2:211319939		T>I	A:100	(-15.30, 156.12, 178.69)
2:211319933	rs371433604 COSM2715566	R>H	A:102	(-14.92, 160.91, 179.85)
2:211319934		R>C	A:102	(-14.92, 160.91, 179.85)
2:211319925		T>A	A:105	(-5.09, 159.70, 175.28)
2:211319908		D>E	A:110	(-10.46, 154.88, 175.06)
2:211319909		D>V	A:110	(-10.46, 154.88, 175.06)
2:211319900	rs562369667	P>L	A:113	(-7.04, 150.42, 175.49)
2:211319895		A>S	A:115	(-3.54, 150.13, 170.56)
2:211319889		A>T	A:117	(-5.10, 145.46, 171.62)
2:211319886	rs370249839	A>T	A:118	(-4.06, 145.70, 168.27)
2:211319874	rs151334050	H>N	A:122	(-0.28, 141.36, 164.79)
2:211319865	COSM271353	N>D	A:125	(-1.66, 135.44, 164.55)
2:211319861		N>I	A:126	(-6.74, 137.75, 166.13)
2:211319857		E>D	A:127	(-5.61, 139.87, 161.91)
2:211319849		A>E	A:130	(-6.96, 143.88, 165.25)
2:211319850		A>T	A:130	(-6.96, 143.88, 165.25)
2:211319841		C>R	A:133	(-9.32, 147.61, 167.13)
2:211319831		R>Q	A:136	(-13.30, 150.18, 168.74)
2:211306161	rs142557584	I>M	A:138	(-9.33, 155.56, 163.08)
2:211306159		H>R	A:139	(-14.35, 155.86, 163.96)
2:211306157		L>V	A:140	(-11.45, 157.58, 169.25)
2:211306144	rs369029984	D>G	A:144	(-12.78, 166.02, 171.57)
2:211306138	rs202027938	H>P	A:146	(-13.11, 171.71, 170.45)
2:211306139	rs568983336	H>Y	A:146	(-13.11, 171.71, 170.45)
2:211306135	rs139476683	A>D	A:147	(-8.81, 168.91, 172.04)
2:211306111	rs150808869	R>Q	A:155	(-5.11, 167.42, 169.21)
2:211306109		I>V	A:156	(0.46, 164.72, 171.03)
2:211306105		G>A	A:157	(-1.43, 161.35, 172.61)
2:211306106	rs141236725	G>S	A:157	(-1.43, 161.35, 172.61)
2:211306094		A>T	A:161	(-1.56, 155.49, 169.47)
2:211306091	rs182044267	L>F	A:162	(-1.99, 156.59, 165.75)
2:211306083	rs143543405	F>L	A:164	(2.21, 151.32, 169.93)
2:211306078	rs75174340	N>S	A:166	(2.00, 152.21, 162.16)
2:211306079		N>D	A:166	(2.00, 152.21, 162.16)
2:211306069		F>S	A:169	(0.86, 145.97, 163.07)
2:211306063		V>A	A:171	(2.80, 148.13, 157.32)
2:211306055	rs369706201	I>F	A:174	(-2.79, 154.24, 160.66)
2:211306038		I>M	A:179	(-1.21, 161.25, 161.08)
2:211306039		I>T	A:179	(-1.21, 161.25, 161.08)
2:211305462		E>K	A:184	(-2.21, 170.15, 159.26)
2:211305434		L>Q	A:193	(-3.34, 180.73, 171.14)
2:211305426		K>E	A:196	(-6.62, 184.62, 170.07)
2:211305416		F>S	A:199	(3.13, 184.67, 173.31)
2:211305413	rs141178650	T>M	A:200	(3.20, 186.24, 167.30)
2:211305408		K>E	A:202	(7.69, 186.57, 172.44)
2:211305402	rs200162143	P>S	A:204	(5.44, 181.49, 166.40)
2:211305394		M>I	A:206	(1.47, 179.03, 172.40)
2:211305395		M>T	A:206	(1.47, 179.03, 172.40)
2:211305392		Y>C	A:207	(0.31, 175.01, 171.79)
2:211305357		H>Y	A:219	(0.16, 168.37, 180.76)
2:211305338		Y>F	A:225	(7.03, 172.66, 170.38)
2:211305333		Y>H	A:227	(5.32, 163.92, 169.41)
2:211305322		Q>H	A:230	(9.35, 163.40, 165.33)
2:211302595		P>L	A:231	(10.09, 162.73, 161.20)
2:211302590		L>F	A:233	(4.26, 164.15, 162.47)
2:211302584		V>L	A:235	(6.41, 169.43, 159.36)
2:211302579		S>R	A:236	(7.01, 171.59, 156.09)
2:211302577		Q>P	A:237	(12.09, 171.80, 156.08)
2:211302567		L>F	A:240	(10.17, 172.76, 160.67)
2:211302565		H>L	A:241	(13.36, 176.17, 159.78)
2:211302554		K>E	A:245	(13.87, 176.94, 165.30)
2:211302545		V>I	A:248	(11.96, 175.51, 170.54)
2:211302540		D>E	A:249	(14.42, 178.87, 170.27)
2:211302539		Y>H	A:250	(9.63, 181.33, 174.52)
2:211302514		S>F	A:258	(19.77, 175.57, 187.00)
2:211302503		P>S	A:262	(9.69, 176.26, 184.07)
2:211302490		G>D	A:266	(6.42, 182.50, 185.24)
2:211302486		D>E	A:267	(6.61, 179.45, 187.21)
2:211302487		D>G	A:267	(6.61, 179.45, 187.21)
2:211302479	rs144579426	D>Y	A:270	(13.89, 175.70, 190.46)
2:211302461		C>R	A:276	(6.00, 166.02, 184.09)
2:211302452	rs149749262	A>T	A:279	(14.41, 168.50, 182.57)
2:211302446		G>R	A:281	(11.15, 166.43, 179.35)
2:211302443		V>I	A:282	(12.62, 169.63, 178.25)
2:211302432		M>I	A:285	(12.76, 169.82, 172.94)
2:211302434		M>V	A:285	(12.76, 169.82, 172.94)
2:211302430	rs371454243	L>P	A:286	(16.67, 170.04, 173.80)
2:211302431		L>V	A:286	(16.67, 170.04, 173.80)
2:211301115	rs6723823	V>E	A:292	(16.22, 168.47, 163.12)
2:211301116		V>L	A:292	(16.22, 168.47, 163.12)
2:211301100	rs147390013	K>M	A:297	(21.81, 176.18, 170.69)
2:211301101		K>E	A:297	(21.81, 176.18, 170.69)
2:211301098		Y>H	A:298	(19.19, 173.42, 170.02)
2:211301091		C>Y	A:300	(24.54, 172.43, 175.14)
2:211301082	rs373538841	Y>C	A:303	(25.69, 167.46, 177.06)
2:211301077	rs200558329	C>R	A:305	(19.59, 168.64, 181.55)
2:211301068	rs148198424	V>M	A:308	(20.21, 168.95, 186.70)
2:211301055	rs143380318	Y>C	A:312	(19.57, 168.36, 192.10)
2:211301046		L>P	A:315	(12.97, 162.10, 193.18)
2:211301040		K>R	A:317	(7.59, 162.21, 194.58)
2:211301032		G>R	A:320	(9.00, 156.63, 188.54)
2:211301029		L>V	A:321	(8.22, 156.61, 184.50)
2:211301026		C>G	A:322	(5.87, 160.90, 185.71)
2:211301020	rs200373437	G>S	A:324	(11.07, 159.69, 189.02)
2:211301011	COSM1691906	G>W	A:327	(12.42, 158.54, 184.26)
2:211301005		A>S	A:329	(17.14, 157.75, 183.64)
2:211301001		Y>C	A:330	(14.12, 156.05, 180.19)
2:211300974	rs368641862	T>I	A:339	(26.50, 160.65, 172.32)
2:211300964	rs548131574	M>I	A:342	(29.86, 155.18, 177.41)
2:211300966		M>V	A:342	(29.86, 155.18, 177.41)
2:211300962		K>M	A:343	(29.28, 160.52, 181.29)
2:211300180	rs370816113	A>S	A:352	(19.40, 151.38, 188.49)
2:211300161	rs370723275	Y>F	A:358	(11.23, 149.81, 194.94)
2:211300162		Y>N	A:358	(11.23, 149.81, 194.94)
2:211300149		G>V	A:362	(11.67, 156.26, 202.46)
2:211300138		P>A	A:366	(2.84, 155.23, 195.11)
2:211300131		T>I	A:368	(-1.28, 153.80, 191.55)
2:211300122		S>C	A:371	(1.40, 151.99, 188.02)
2:211299243		T>S	A:390	(20.58, 150.56, 171.87)
2:211299232		R>S	A:393	(13.26, 154.10, 172.99)
2:211299217		E>D	A:398	(11.20, 158.54, 173.29)
2:211299215		L>P	A:399	(9.16, 157.83, 168.75)

3E6U.A | LANCL1.

3E6U.A | LANCL1

General Structure Information

Variant Set Distributions

Ripley’s K Analysis Plots

Variant Set Comparisons

Pathogenic Proximity Analysis

Mapped Variants

[+] ExAC Missense Variants

[+] COSMIC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
2:211336761	COSM209839	R>W	A:41	(12.81, 136.91, 187.27)
2:211336712	COSM2715570	R>Q	A:57	(-14.16, 149.83, 186.15)
2:211306111	COSM1015856	R>Q	A:155	(-5.11, 167.42, 169.21)
2:211302499	COSM3577059	P>L	A:263	(6.42, 174.37, 185.52)