1DC2.A | CDKN2A

General Structure Information

PDB ID	1dc2
HGNC Gene Label(s)	CDKN2A
Structure Name	solution nmr structure of tumor suppressor p16ink4a, 20 structures
Resolution	-1.0Å
Reference	AUTH C.YUAN,T.L.SELBY,J.LI,I.J.BYEON,M.D.TSAITITL TUMOR SUPPRESSOR INK4: REFINEMENT OF P16INK4ATITL 2 STRUCTURE AND DETERMINATION OF P15INK4B STRUCTURETITL 3 BY COMPARATIVE MODELING AND NMR DATA.REF PROTEIN SCI. V. 9 1120 2000REFN ISSN 0961-8368PMID 10892805

Variant Set Distributions

ExAC Variants

Number Of Residues	156
Number Of SNVs	47
Number Of Permutations	14903
Optimal Distance Threshold	11.0
K Statistic	0.154
p-value	0.459

ClinVar

Number Of Residues	156
Number Of SNVs	13
Number Of Permutations	3602
Optimal Distance Threshold	21.0
K Statistic	0.846
p-value	0.023

COSMIC

Number Of Residues	156
Number Of SNVs	47
Number Of Permutations	50443
Optimal Distance Threshold	22.0
K Statistic	0.708
p-value	0.002

Ripley’s K Analysis Plots

ExACClinVarCOSMIC

Variant Set Comparisons

ClinVar vs. ExAC

Number Of ExAC SNVs	47
Number Of ClinVar SNVs	11
Optimal Distance Threshold	18.0
K Statistic	0.291
p-value	0.128

Cosmic vs. ExAC

Number Of ExAC SNVs	47
Number Of COSMIC SNVs	17
Optimal Distance Threshold	20.0
K Statistic	0.178
p-value	0.245

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
9:21974802		M>L	A:9	(12.39, 20.67, -14.16)
9:21974789	COSM3724570	A>V	A:13	(1.23, 15.75, -20.67)
9:21974784		W>R	A:15	(-2.95, 18.21, -16.23)
9:21974774	rs560518923 COSM13626	T>K	A:18	(-2.37, 12.84, -11.99)
9:21974775	COSM238571 COSM238572	T>P	A:18	(-2.37, 12.84, -11.99)
9:21974769	COSM12761 COSM13537 COSM13521	A>S	A:20	(-7.10, 8.46, -12.80)
9:21974757		R>G	A:24	(-11.21, 13.70, -8.42)
9:21974753	COSM1645941 COSM1645940 COSM1645939	V>G	A:25	(-14.13, 9.46, -13.12)
9:21974744	COSM12489 CM024658	V>G	A:28	(-10.07, 11.84, -16.15)
9:21974733		L>V	A:32	(-9.53, 12.04, -21.97)
9:21974712		N>H	A:39	(-0.88, 7.67, -25.69)
9:21974705	rs373407950	P>Q	A:41	(4.36, 8.58, -21.07)
9:21974706		P>A	A:41	(4.36, 8.58, -21.07)
9:21974684	COSM12743 COSM13272 COSM3092328 COSM3930002 COSM3930001 COSM3092327 CM970251	P>R	A:48	(-2.29, 5.92, -18.99)
9:21974681	rs199907548 COSM3395762 COSM13545 COSM303861 COSM303862 COSM3395761 COSM3685582 COSM3395760 COSM3685	I>T	A:49	(-5.52, 2.70, -17.97)
9:21971203	COSM13436 COSM48952 COSM608437 COSM608435 COSM608436 COSM1650883	M>T	A:52	(-7.11, 3.23, -13.29)
9:21971199	rs104894095	M>I	A:53	(-7.76, 4.21, -7.92)
9:21971196		M>I	A:54	(-6.57, -0.16, -11.19)
9:21971198	rs201314211	M>L	A:54	(-6.57, -0.16, -11.19)
9:21971190	COSM13467	S>R	A:56	(-12.53, 3.81, -10.93)
9:21971182	rs104894099	V>G	A:59	(-11.08, 6.22, -14.84)
9:21971180	COSM13720	A>T	A:60	(-10.43, 2.66, -17.68)
9:21971161	COSM14253 COSM28561 CM994793 CM034775	H>R	A:66	(-10.41, 8.88, -25.28)
9:21971159	COSM12746 CM013694 CM994399	G>S	A:67	(-6.53, 5.62, -26.25)
9:21971152	rs372670098 COSM13717 CM065061	E>G	A:69	(-0.88, 3.06, -22.92)
9:21971146	rs559848002 COSM13710 CM112063 CM940228 CM983987	N>S	A:71	(-1.49, -2.94, -24.91)
9:21971134	COSM12490 COSM12510	P>L	A:75	(10.53, -1.21, -19.18)
9:21971120	rs121913388 COSM12475 COSM99935 COSM99191 COSM1314729 CM014695	R>G	A:80	(2.02, -5.34, -20.24)
9:21971099	COSM231512 COSM13680 COSM231513 COSM1461808 COSM1461810 COSM231514 COSM1461809 CM024659 CM990359	R>W	A:87	(-3.46, -5.50, -6.96)
9:21971093	rs137854597	G>S	A:89	(-10.07, -6.88, -8.18)
9:21971060	rs200863613 COSM12513 COSM13772 CX024722	A>S	A:100	(-9.91, -1.80, -26.51)
9:21971056		G>E	A:101	(-7.65, -4.54, -27.90)
9:21971057	rs104894094 COSM48298 CM940230 CM043784	G>R	A:101	(-7.65, -4.54, -27.90)
9:21971051		R>W	A:103	(-0.70, -9.03, -25.23)
9:21971042	COSM13505	V>L	A:106	(2.13, -9.79, -20.70)
9:21971038	rs370823171 COSM1200606 COSM1200604 COSM1200605	R>H	A:107	(6.74, -13.03, -19.17)
9:21971033	rs372481694 COSM12752	A>P	A:109	(8.76, -10.29, -15.45)
9:21971030		W>G	A:110	(10.40, -10.48, -11.80)
9:21971023	COSM13811 COSM3433073 COSM3433070 COSM3433072 COSM3433071	R>L	A:112	(4.49, -17.63, -12.45)
9:21971015	COSM13227 COSM308277 COSM308278	V>M	A:115	(-4.32, -15.33, -14.71)
9:21970998		E>D	A:120	(-1.67, -16.18, -5.80)
9:21970987	COSM13608 COSM1200603 COSM1569309	R>H	A:124	(-11.17, -17.21, -6.30)
9:21970985	rs146179135	D>H	A:125	(-14.00, -12.98, -9.45)
9:21970967	COSM20968 COSM3906635 COSM3906634	R>C	A:131	(-6.75, -19.46, -15.97)
9:21970957	COSM13612	A>V	A:134	(-5.60, -14.37, -20.99)
9:21970958	rs372599739	A>P	A:134	(-5.60, -14.37, -20.99)
9:21970951	COSM13790	G>D	A:136	(-3.27, -20.44, -22.34)
9:21970952	COSM33803	G>S	A:136	(-3.27, -20.44, -22.34)
9:21970942	rs149937815	G>D	A:139	(1.60, -23.59, -28.42)
9:21970943		G>R	A:139	(1.60, -23.59, -28.42)
9:21970933		H>R	A:142	(2.38, -32.43, -27.56)
9:21970930		A>G	A:143	(2.34, -33.11, -22.76)
9:21970931	COSM13977	A>T	A:143	(2.34, -33.11, -22.76)
9:21970928	rs116150891	R>C	A:144	(-2.60, -29.44, -20.89)
9:21970916	rs3731249	A>T	A:148	(7.33, -33.90, -19.85)

[+] ClinVar Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
9:21974756	rs104894097	R>Q	A:24	(-11.21, 13.70, -8.42)
9:21974685	rs786204195	P>T	A:48	(-2.29, 5.92, -18.99)
9:21971199	rs104894095	M>I	A:53	(-7.76, 4.21, -7.92)
9:21971191	rs104894109	S>I	A:56	(-12.53, 3.81, -10.93)
9:21971182	rs104894099	V>G	A:59	(-11.08, 6.22, -14.84)
9:21971179	rs36204594	A>V	A:60	(-10.43, 2.66, -17.68)
9:21971152	rs372670098	E>G	A:69	(-0.88, 3.06, -22.92)
9:21971093	rs137854597	G>S	A:89	(-10.07, -6.88, -8.18)
9:21971057	rs104894094	G>W	A:101	(-7.65, -4.54, -27.90)
9:21971036	rs121913381	D>Y	A:108	(4.50, -9.32, -14.40)
9:21971017	rs387906410	LP>LS	A:114	(-1.90, -11.25, -15.40)
9:21970994	rs113798404	G>S	A:122	(-7.65, -12.26, -4.22)
9:21970981	rs104894098	V>D	A:126	(-10.32, -10.72, -11.70)

[+] COSMIC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
9:21974814	COSM12742	A>T	A:5	(23.30, 18.39, -14.17)
9:21974800	COSM13542	M>I	A:9	(12.39, 20.67, -14.16)
9:21974785	COSM13536	D>E	A:14	(0.84, 13.88, -16.30)
9:21974783	COSM13751	W>L	A:15	(-2.95, 18.21, -16.23)
9:21974780	COSM13543	L>P	A:16	(-4.30, 12.03, -18.72)
9:21974768	COSM1648136	A>E	A:20	(-7.10, 8.46, -12.80)
9:21974769	COSM13521	A>P	A:20	(-7.10, 8.46, -12.80)
9:21974765	COSM13631	A>D	A:21	(-4.59, 7.72, -9.69)
9:21974756	COSM4951075	R>P	A:24	(-11.21, 13.70, -8.42)
9:21974753	COSM1645941	V>G	A:25	(-14.13, 9.46, -13.12)
9:21974751	COSM13273	E>K	A:26	(-15.74, 14.11, -12.36)
9:21974738	COSM13685	A>V	A:30	(-13.30, 17.08, -18.12)
9:21974726	COSM13650	A>V	A:34	(-9.95, 18.91, -22.59)
9:21974723	COSM13259	G>E	A:35	(-7.21, 17.14, -24.76)
9:21974724	COSM13277	G>R	A:35	(-7.21, 17.14, -24.76)
9:21974720	COSM3926637	A>G	A:36	(-6.18, 14.70, -22.24)
9:21974708	COSM20971	A>V	A:40	(0.61, 10.50, -21.69)
9:21974699	COSM13653	S>I	A:43	(7.00, 9.77, -13.85)
9:21974693	COSM33786	G>D	A:45	(5.61, 3.87, -14.59)
9:21974684	COSM3092328	P>L	A:48	(-2.29, 5.92, -18.99)
9:21974681	COSM3395762	I>N	A:49	(-5.52, 2.70, -17.97)
9:21971206	COSM13276	V>A	A:51	(-1.70, 5.35, -12.63)
9:21971207	COSM13496	V>I	A:51	(-1.70, 5.35, -12.63)
9:21971203	COSM608436	M>R	A:52	(-7.11, 3.23, -13.29)
9:21971188	COSM4384417	A>V	A:57	(-13.46, 0.82, -14.18)
9:21971189	COSM310018	A>T	A:57	(-13.46, 0.82, -14.18)
9:21971179	COSM22560	A>V	A:60	(-10.43, 2.66, -17.68)
9:21971171	COSM13782	L>V	A:63	(-7.45, 7.19, -20.20)
9:21971164	COSM13972	L>P	A:65	(-13.06, 5.69, -24.73)
9:21971158	COSM1107902	G>D	A:67	(-6.53, 5.62, -26.25)
9:21971155	COSM12744	A>E	A:68	(-5.02, 4.48, -23.17)
9:21971153	COSM13651	E>Q	A:69	(-0.88, 3.06, -22.92)
9:21971149	COSM13815	P>L	A:70	(-4.52, -0.72, -23.07)
9:21971145	COSM22561	N>K	A:71	(-1.49, -2.94, -24.91)
9:21971136	COSM13768	D>E	A:74	(6.86, -1.41, -16.87)
9:21971137	COSM4163710	D>A	A:74	(6.86, -1.41, -16.87)
9:21971138	COSM12509	D>Y	A:74	(6.86, -1.41, -16.87)
9:21971134	COSM12510	P>H	A:75	(10.53, -1.21, -19.18)
9:21971131	COSM13766	A>V	A:76	(11.39, -3.01, -15.32)
9:21971132	COSM1200601	A>T	A:76	(11.39, -3.01, -15.32)
9:21971122	COSM12468	T>I	A:79	(3.76, -3.96, -14.47)
9:21971119	COSM3906647	R>Q	A:80	(2.02, -5.34, -20.24)
9:21971116	COSM3092301	P>L	A:81	(-2.41, -2.69, -18.29)
9:21971117	COSM48299	P>S	A:81	(-2.41, -2.69, -18.29)
9:21971114	COSM12469	V>M	A:82	(-3.58, -7.23, -17.61)
9:21971111	COSM4388670	H>D	A:83	(-0.71, -7.75, -14.07)
9:21971107	COSM608441	D>V	A:84	(-3.42, -2.87, -12.41)
9:21971108	COSM3355721	HD>PD	A:84	(-3.42, -2.87, -12.41)
9:21971099	COSM1461809	R>W	A:87	(-3.46, -5.50, -6.96)
9:21971094	COSM13539	E>D	A:88	(-6.80, -3.50, -7.52)
9:21971095	COSM13688	RE>RK	A:88	(-6.80, -3.50, -7.52)
9:21971096	COSM1167919	E>K	A:88	(-6.80, -3.50, -7.52)
9:21971092	COSM13472	G>V	A:89	(-10.07, -6.88, -8.18)
9:21971090	COSM13264	F>L	A:90	(-12.26, -2.76, -10.52)
9:21971086	COSM13636	L>Q	A:91	(-13.81, -8.48, -13.67)
9:21971080	COSM4604971	T>K	A:93	(-10.40, -2.64, -15.36)
9:21971068	COSM13780	L>P	A:97	(-7.76, -3.55, -20.54)
9:21971065	COSM4781708	H>P	A:98	(-10.70, -8.22, -23.88)
9:21971062	COSM342060	R>P	A:99	(-15.75, -3.22, -23.90)
9:21971063	COSM12756	R>W	A:99	(-15.75, -3.22, -23.90)
9:21971059	COSM3092278	A>V	A:100	(-9.91, -1.80, -26.51)
9:21971060	COSM12513	A>S	A:100	(-9.91, -1.80, -26.51)
9:21971057	COSM3092275	G>W	A:101	(-7.65, -4.54, -27.90)
9:21971053	COSM13675	A>V	A:102	(-6.40, -5.97, -24.56)
9:21971047	COSM3780729	L>Q	A:104	(-5.86, -10.10, -21.38)
9:21971042	COSM13505	V>M	A:106	(2.13, -9.79, -20.70)
9:21971039	COSM4993343	R>C	A:107	(6.74, -13.03, -19.17)
9:21971035	COSM4767456	D>A	A:108	(4.50, -9.32, -14.40)
9:21971036	COSM753738	D>Y	A:108	(4.50, -9.32, -14.40)
9:21971023	COSM3433070	R>H	A:112	(4.49, -17.63, -12.45)
9:21971024	COSM13644	R>S	A:112	(4.49, -17.63, -12.45)
9:21971017	COSM4408167	P>R	A:114	(-1.90, -11.25, -15.40)
9:21971015	COSM308277	V>L	A:115	(-4.32, -15.33, -14.71)
9:21971012	COSM13807	D>Y	A:116	(-1.37, -16.47, -11.93)
9:21971000	COSM13296	E>K	A:120	(-1.67, -16.18, -5.80)
9:21970993	COSM4384412	G>D	A:122	(-7.65, -12.26, -4.22)
9:21970989	COSM13463	H>Q	A:123	(-8.01, -10.43, -7.08)
9:21970987	COSM1200603	R>H	A:124	(-11.17, -17.21, -6.30)
9:21970981	COSM3906636	V>D	A:126	(-10.32, -10.72, -11.70)
9:21970982	COSM13294	V>F	A:126	(-10.32, -10.72, -11.70)
9:21970975	COSM1461802	R>Q	A:128	(-12.58, -18.38, -12.40)
9:21970976	COSM4998308	R>W	A:128	(-12.58, -18.38, -12.40)
9:21970972	COSM13633	Y>C	A:129	(-13.05, -12.55, -17.29)
9:21970969	COSM3788240	L>P	A:130	(-7.55, -12.58, -16.00)
9:21970966	COSM1461801	R>H	A:131	(-6.75, -19.46, -15.97)
9:21970967	COSM20968	R>C	A:131	(-6.75, -19.46, -15.97)
9:21970964	COSM13298	A>P	A:132	(-10.98, -16.90, -20.05)
9:21970945	COSM13708	R>T	A:138	(-0.57, -19.06, -27.08)
9:21970916	COSM3774362	A>T	A:148	(7.33, -33.90, -19.85)