1KV3.B | TGM2 – ASTRID

1KV3.B | TGM2

General Structure Information

PDB ID	1kv3
HGNC Gene Label(s)	TGM2
Structure Name	human tissue transglutaminase in gdp bound form
Resolution	2.8Å
Reference	AUTH S.LIU,R.A.CERIONE,J.CLARDYTITL STRUCTURAL BASIS FOR THE GUANINETITL 2 NUCLEOTIDE-BINDING ACTIVITY OF TISSUETITL 3 TRANSGLUTAMINASE AND ITS REGULATION OFTITL 4 TRANSAMIDATION ACTIVITY.REF PROC.NATL.ACAD.SCI.USA V. 99 2743 2002REFN ISSN 0027-8424PMID 11867708DOI 10.1073/PNAS.042454899

Variant Set Distributions

ExAC Variants

Number Of Residues	651
Number Of SNVs	174
Number Of Permutations	83993
Optimal Distance Threshold	6.0
K Statistic	0.006
p-value	0.218

COSMIC

Number Of Residues	651
Number Of SNVs	9
Number Of Permutations	8303
Optimal Distance Threshold	14.0
K Statistic	0.028
p-value	0.872

Ripley’s K Analysis Plots

ExACCOSMIC

Variant Set Comparisons

Cosmic vs. ExAC

Number Of ExAC SNVs	174
Number Of COSMIC SNVs	8
Optimal Distance Threshold	14.0
K Statistic	-0.067
p-value	0.865

Pathogenic Proximity Analysis

COSMIC PathProx Analysis

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
20:36789969		E>K	B:15	(48.15, 55.42, 203.90)
20:36789956	COSM3911266	R>Q	B:19	(40.96, 57.84, 205.11)
20:36789944	rs147890243	T>M	B:23	(44.26, 52.41, 211.89)
20:36789942		A>T	B:24	(46.15, 56.14, 211.27)
20:36789929		R>L	B:28	(52.84, 56.71, 211.63)
20:36789930		R>W	B:28	(52.84, 56.71, 211.63)
20:36789911		R>Q	B:34	(40.35, 47.64, 212.51)
20:36789909		R>W	B:35	(37.74, 41.08, 212.66)
20:36789901	rs375639089	Q>H	B:37	(37.21, 46.47, 206.43)
20:36789892	rs563361176	W>C	B:40	(42.16, 49.78, 198.31)
20:36789884	rs541651912	L>R	B:43	(51.43, 45.16, 193.01)
20:36789834	rs370982887	S>G	B:60	(49.48, 33.45, 201.57)
20:36789828	rs199577232	V>M	B:62	(50.74, 33.06, 208.29)
20:36789822	rs376529551	G>S	B:64	(51.48, 32.10, 213.97)
20:36784486		A>T	B:66	(51.61, 27.10, 214.25)
20:36784479	rs181404288	S>I	B:68	(46.26, 25.91, 210.55)
20:36784468		G>R	B:72	(42.49, 30.17, 210.94)
20:36784459		A>S	B:75	(45.14, 31.40, 204.33)
20:36784455	rs41274720	R>H	B:76	(46.93, 29.10, 199.90)
20:36784456	rs376510500 COSM3911263	R>C	B:76	(46.93, 29.10, 199.90)
20:36784449	rs61733919	P>L	B:78	(42.42, 32.92, 194.86)
20:36784446		L>P	B:79	(43.85, 37.21, 192.00)
20:36784441		D>H	B:81	(37.91, 39.40, 188.69)
20:36784435		V>M	B:83	(33.67, 37.65, 194.99)
20:36784408	rs139395066	V>M	B:92	(41.07, 42.75, 190.65)
20:36784404		V>G	B:93	(40.01, 46.96, 190.96)
20:36784386		T>I	B:99	(50.26, 49.24, 188.31)
20:36784374	rs377161987	Q>R	B:103	(40.03, 45.13, 197.45)
20:36784365	rs141500725	T>I	B:106	(39.60, 39.92, 206.25)
20:36784362		P>L	B:107	(37.58, 37.15, 207.93)
20:36784363		P>S	B:107	(37.58, 37.15, 207.93)
20:36784354	rs146137365	A>T	B:110	(39.67, 36.74, 212.10)
20:36784350	rs141628501	P>R	B:111	(42.34, 35.49, 213.82)
20:36784345	COSM1664547	G>S	B:113	(47.44, 39.82, 214.56)
20:36784336	rs138618726	R>C	B:116	(54.57, 36.17, 208.32)
20:36784317	rs545792168	S>C	B:122	(52.64, 31.07, 187.05)
20:36784271		L>F	B:137	(43.87, 41.74, 211.81)
20:36779453	rs138064359	A>V	B:147	(31.50, 40.67, 217.71)
20:36779454	rs149036689	A>T	B:147	(31.50, 40.67, 217.71)
20:36779438		S>L	B:152	(27.33, 54.31, 217.15)
20:36779426		R>Q	B:156	(31.97, 53.25, 216.32)
20:36779427	rs373810330	R>W	B:156	(31.97, 53.25, 216.32)
20:36779408		T>N	B:162	(39.15, 58.22, 222.65)
20:36779409		T>A	B:162	(39.15, 58.22, 222.65)
20:36779394		I>L	B:167	(39.48, 57.06, 236.56)
20:36779381		S>L	B:171	(33.05, 59.69, 247.57)
20:36779367	rs200959101	K>Q	B:176	(37.14, 63.80, 242.07)
20:36779363	COSM1411649	N>S	B:177	(37.30, 63.73, 237.62)
20:36779358		P>A	B:179	(42.98, 62.53, 234.87)
20:36776443		P>T	B:201	(49.82, 31.44, 230.21)
20:36776422	rs377603006	G>S	B:208	(48.02, 27.37, 218.50)
20:36776418	COSM1483618	R>H	B:209	(44.42, 25.34, 220.42)
20:36776419		R>C	B:209	(44.42, 25.34, 220.42)
20:36776407	COSM1229104	R>C	B:213	(41.15, 29.04, 221.44)
20:36776403	rs45530133	R>H	B:214	(44.98, 35.46, 219.78)
20:36776391		V>A	B:218	(35.60, 36.41, 225.25)
20:36776386	rs373772486	V>M	B:220	(41.31, 38.50, 224.00)
20:36776379	rs200551434	R>Q	B:222	(39.19, 34.99, 230.59)
20:36776370		S>N	B:225	(42.40, 40.43, 232.56)
20:36775289		C>Y	B:230	(47.08, 37.50, 238.07)
20:36775279		D>E	B:233	(55.68, 35.03, 236.36)
20:36775259		R>H	B:240	(52.76, 47.63, 248.19)
20:36775260	rs372703574	R>C	B:240	(52.76, 47.63, 248.19)
20:36775247		N>S	B:244	(55.47, 51.70, 251.91)
20:36775248		N>D	B:244	(55.47, 51.70, 251.91)
20:36775242	rs556495732	G>R	B:246	(59.32, 54.04, 247.43)
20:36775235		G>D	B:248	(58.38, 53.12, 243.41)
20:36775233		V>I	B:249	(55.38, 54.28, 241.10)
20:36775226		P>R	B:251	(49.43, 53.63, 242.94)
20:36775212	rs371462067 COSM251162	G>S	B:256	(48.87, 56.33, 232.52)
20:36775209		S>R	B:257	(48.73, 53.17, 230.57)
20:36775193	COSM129694	R>Q	B:262	(56.43, 52.66, 227.05)
20:36775190	rs191236574	R>H	B:263	(58.32, 51.73, 233.80)
20:36775191		R>C	B:263	(58.32, 51.73, 233.80)
20:36775176		G>S	B:268	(61.21, 41.58, 230.82)
20:36775169		Q>P	B:270	(60.11, 42.09, 235.60)
20:36775166		R>H	B:271	(54.60, 41.60, 239.00)
20:36775164		V>I	B:272	(55.31, 47.52, 237.35)
20:36775154	rs370510175	G>A	B:275	(49.13, 48.90, 241.86)
20:36775134		A>T	B:282	(43.39, 51.22, 232.92)
20:36775131	rs533343230	V>M	B:283	(46.18, 48.90, 231.70)
20:36775121	rs377487569	T>I	B:286	(44.95, 50.64, 226.96)
20:36770578		T>A	B:295	(36.70, 49.23, 226.66)
20:36770574	COSM1026594	R>H	B:296	(32.46, 51.50, 229.64)
20:36770575	COSM1716510 COSM1229100	R>C	B:296	(32.46, 51.50, 229.64)
20:36770569	COSM1411645	V>M	B:298	(33.55, 51.23, 235.73)
20:36770559		Y>C	B:301	(31.62, 55.01, 244.25)
20:36770553		S>L	B:303	(32.31, 47.77, 246.62)
20:36770543		D>E	B:306	(37.78, 40.33, 248.46)
20:36770538		N>S	B:308	(33.72, 34.25, 248.56)
20:36770531		N>K	B:310	(28.69, 36.94, 251.04)
20:36770530		L>F	B:311	(24.86, 38.34, 249.13)
20:36770521	rs138412064	E>K	B:314	(27.42, 39.71, 259.59)
20:36770511	rs138570848	R>H	B:317	(30.62, 48.04, 264.79)
20:36770512	COSM1411644	R>C	B:317	(30.62, 48.04, 264.79)
20:36770502		F>S	B:320	(32.74, 53.56, 272.16)
20:36770487		G>D	B:325	(38.90, 42.64, 264.23)
20:36770476		E>K	B:329	(37.33, 42.71, 253.55)
20:36769773		W>L	B:337	(34.07, 46.99, 237.64)
20:36769749	rs374172551	P>L	B:345	(28.54, 33.25, 221.38)
20:36769725		G>V	B:353	(27.30, 43.76, 225.19)
20:36769704	rs368689999 COSM1229101	T>M	B:360	(41.17, 42.93, 240.72)
20:36769687	rs147979857	E>K	B:366	(38.36, 26.79, 243.02)
20:36768053	rs372235586	T>M	B:368	(43.03, 34.06, 244.01)
20:36768047		C>Y	B:370	(40.26, 37.26, 237.76)
20:36768026	rs78619991	R>H	B:377	(20.67, 41.56, 230.45)
20:36768021		I>L	B:379	(24.58, 41.02, 237.02)
20:36768017		K>R	B:380	(19.75, 44.46, 235.78)
20:36768011	rs371454120	G>D	B:382	(20.12, 37.33, 238.43)
20:36768009	rs137876403	D>N	B:383	(21.39, 34.80, 235.27)
20:36767987		A>V	B:390	(28.19, 36.35, 238.24)
20:36767985		P>A	B:391	(28.38, 35.37, 241.48)
20:36767972	rs138957593	A>V	B:395	(27.96, 41.25, 245.22)
20:36767954	rs201212727	V>E	B:401	(25.68, 45.25, 255.51)
20:36767955		V>M	B:401	(25.68, 45.25, 255.51)
20:36767931	rs368135396 COSM1411642	D>N	B:409	(26.28, 39.34, 278.84)
20:36767927		G>E	B:410	(27.55, 39.20, 274.85)
20:36767915		K>T	B:414	(20.22, 44.30, 264.28)
20:36767909		I>T	B:416	(19.43, 51.33, 262.76)
20:36767903		R>H	B:418	(18.73, 54.74, 258.28)
20:36767849		R>Q	B:436	(29.05, 61.23, 236.37)
20:36767850	rs45629036	R>W	B:436	(29.05, 61.23, 236.37)
20:36767840		I>T	B:439	(26.28, 53.00, 234.64)
20:36767835		H>Y	B:441	(20.83, 52.32, 234.55)
20:36767817		E>K	B:447	(15.89, 50.77, 245.85)
20:36766778		E>A	B:451	(11.51, 44.86, 238.01)
20:36766748		H>R	B:461	(19.52, 38.66, 247.63)
20:36766746		L>V	B:462	(14.34, 37.50, 248.49)
20:36766724	rs139974885	E>G	B:469	(13.71, 48.90, 263.96)
20:36766719		T>A	B:471	(13.74, 55.14, 267.16)
20:36766703	rs574234671	R>Q	B:476	(22.42, 63.13, 257.91)
20:36766700		I>N	B:477	(27.66, 62.46, 258.73)
20:36766697		R>H	B:478	(24.77, 67.37, 257.35)
20:36766698		R>C	B:478	(24.77, 67.37, 257.35)
20:36766687	rs140523273	Q>H	B:481	(31.78, 73.60, 253.89)
20:36766688		Q>R	B:481	(31.78, 73.60, 253.89)
20:36766659		V>I	B:491	(32.23, 67.23, 260.56)
20:36766649	rs151245834	H>L	B:494	(21.94, 66.35, 261.74)
20:36766643		T>N	B:496	(16.33, 63.74, 263.42)
20:36766640		N>S	B:497	(13.45, 63.70, 267.61)
20:36766632		A>T	B:500	(7.27, 63.54, 271.49)
20:36766598	COSM4136872	A>V	B:511	(37.72, 60.02, 262.93)
20:36766590		V>I	B:514	(40.48, 55.49, 254.95)
20:36766580		N>S	B:517	(41.03, 49.36, 250.29)
20:36766563	rs112578056	E>K	B:523	(41.40, 57.42, 266.40)
20:36766524	rs45556333	P>S	B:536	(10.99, 67.24, 271.43)
20:36760891		P>S	B:543	(30.40, 69.38, 266.46)
20:36760882	rs199832452	I>V	B:546	(38.91, 66.95, 261.50)
20:36760872	rs148045565	E>G	B:549	(49.11, 68.35, 262.79)
20:36760863		R>H	B:552	(50.72, 65.84, 258.73)
20:36760851		T>M	B:556	(45.95, 57.91, 251.69)
20:36760852	rs143549454	T>A	B:556	(45.95, 57.91, 251.69)
20:36760845		S>F	B:558	(42.84, 58.82, 248.27)
20:36760842		N>S	B:559	(42.74, 62.59, 250.01)
20:36760828		R>W	B:564	(32.74, 55.77, 263.95)
20:36760821		L>R	B:566	(27.15, 55.04, 267.85)
20:36760810		P>S	B:570	(19.80, 53.85, 277.18)
20:36760789		L>M	B:577	(25.56, 53.34, 262.72)
20:36760786	rs370803946	A>T	B:578	(26.59, 56.74, 261.04)
20:36760771		Y>H	B:583	(38.38, 64.07, 248.30)
20:36760743	rs150712844	R>Q	B:592	(48.95, 80.07, 230.95)
20:36760744	rs201666703	R>W	B:592	(48.95, 80.07, 230.95)
20:36759630		I>T	B:593	(48.14, 76.73, 226.44)
20:36759612		Q>L	B:599	(50.07, 69.42, 213.03)
20:36759609		K>T	B:600	(55.48, 70.29, 213.96)
20:36759607		R>C	B:601	(54.43, 75.65, 215.68)
20:36759573	rs376514575 COSM3785392	P>L	B:612	(47.96, 73.75, 250.58)
20:36759574	rs199563008	P>T	B:612	(47.96, 73.75, 250.58)
20:36759571		L>I	B:613	(50.32, 72.52, 253.25)
20:36759565		V>L	B:615	(54.23, 73.17, 255.93)
20:36759555		E>A	B:618	(60.90, 69.71, 250.50)
20:36759552	rs371812638	G>D	B:619	(60.39, 67.75, 245.79)
20:36759547		T>A	B:621	(57.83, 66.91, 240.60)
20:36759542	COSM345134	F>L	B:622	(54.76, 69.85, 238.06)
20:36759540		T>I	B:623	(54.49, 64.89, 235.55)
20:36759525	rs200284500	G>A	B:628	(49.28, 64.26, 220.87)
20:36759526	COSM1483617	G>S	B:628	(49.28, 64.26, 220.87)
20:36759519		T>S	B:630	(53.88, 64.30, 223.99)
20:36759517		E>K	B:631	(55.37, 61.01, 221.28)
20:36759504	rs547350980	T>M	B:635	(59.68, 65.64, 234.16)
20:36759498		E>V	B:637	(63.06, 68.14, 239.17)
20:36758763		P>L	B:641	(61.89, 74.87, 248.83)
20:36758754		A>G	B:644	(53.26, 78.01, 252.94)
20:36758755		A>S	B:644	(53.26, 78.01, 252.94)
20:36758718		P>L	B:656	(52.17, 68.86, 218.97)
20:36758716		L>F	B:657	(52.99, 65.09, 216.18)
20:36758712		H>R	B:658	(48.86, 63.71, 216.31)
20:36758694		L>Q	B:664	(47.72, 68.00, 229.03)
20:36758680	rs150186613	E>K	B:669	(54.79, 64.17, 243.82)
20:36758674	rs141236503	D>N	B:671	(57.31, 66.02, 250.89)
20:36758670	rs373793262	K>R	B:672	(54.88, 67.28, 253.06)
20:36758658		V>A	B:676	(48.06, 66.74, 242.56)
20:36758647	rs146621816	R>W	B:680	(43.70, 72.86, 229.03)
20:36758634	rs373901593	I>T	B:684	(45.95, 70.84, 218.04)
20:36758625		A>V	B:687	(49.89, 73.87, 210.13)

1KV3.B | TGM2.

1KV3.B | TGM2

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
20:36789962	COSM1615568	N>S	B:17	(44.21, 51.20, 204.34)
20:36779364	COSM1411650	N>D	B:177	(37.30, 63.73, 237.62)
20:36770569	COSM1411645	V>M	B:298	(33.55, 51.23, 235.73)
20:36770508	COSM1722794	N>I	B:318	(32.99, 48.45, 270.20)
20:36769692	COSM3423633	K>R	B:364	(37.44, 32.91, 243.26)
20:36768026	COSM2154821	R>H	B:377	(20.67, 41.56, 230.45)
20:36766704	COSM723780	R>W	B:476	(22.42, 63.13, 257.91)
20:36766598	COSM4136872	A>V	B:511	(37.72, 60.02, 262.93)
20:36759542	COSM345134	F>L	B:622	(54.76, 69.85, 238.06)