2IFG.A | NTRK1

General Structure Information

PDB ID	2ifg
HGNC Gene Label(s)	NTRK1
Structure Name	structure of the extracellular segment of human trka in complex with nerve growth factor
Resolution	3.4Å
Reference	AUTH T.WEHRMAN,X.HE,B.RAAB,A.DUKIPATTI,H.BLAU,K.C.GARCIATITL STRUCTURAL AND MECHANISTIC INSIGHTS INTO NERVE GROWTH FACTORTITL 2 INTERACTIONS WITH THE TRKA AND P75 RECEPTORS.REF NEURON V. 53 25 2007REFN ISSN 0896-6273PMID 17196528DOI 10.1016/J.NEURON.2006.09.034

Variant Set Distributions

ExAC Variants

Number Of Residues	347
Number Of SNVs	97
Number Of Permutations	32800
Optimal Distance Threshold	26.0
K Statistic	0.345
p-value	0.61

COSMIC

Number Of Residues	347
Number Of SNVs	8
Number Of Permutations	3814
Optimal Distance Threshold	4.0
K Statistic	0.036
p-value	0.206

Ripley’s K Analysis Plots

ExACCOSMIC

Variant Set Comparisons

Cosmic vs. ExAC

Number Of ExAC SNVs	97
Number Of COSMIC SNVs	7
Optimal Distance Threshold	11.0
K Statistic	0.227
p-value	0.084

Pathogenic Proximity Analysis

COSMIC PathProx Analysis

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
1:156830841		A>S	A:39	(-57.30, -21.33, 34.13)
1:156830869		L>P	A:48	(-47.33, -19.08, 32.39)
1:156830871		R>G	A:49	(-49.53, -14.10, 35.22)
1:156830878	rs376870955	T>I	A:51	(-53.29, -16.94, 40.80)
1:156830883	rs200815412	D>H	A:53	(-57.20, -24.35, 40.84)
1:156830899		S>T	A:58	(-53.13, -30.69, 30.88)
1:156830904	rs564537453	H>N	A:60	(-47.15, -30.61, 31.31)
1:156830911		L>P	A:62	(-51.71, -27.97, 24.52)
1:156834148		Y>C	A:72	(-46.66, -15.77, 39.49)
1:156834153		E>K	A:74	(-50.05, -17.30, 43.98)
1:156834169	rs139140006	L>Q	A:79	(-49.70, -29.04, 44.55)
1:156834172	rs55891455	Q>R	A:80	(-49.30, -31.98, 49.10)
1:156834189		D>Y	A:86	(-44.87, -31.52, 38.82)
1:156834198	rs2274496	G>S	A:89	(-40.62, -28.26, 30.83)
1:156834204	rs149646444	G>R	A:91	(-37.18, -24.15, 31.33)
1:156834524		I>V	A:98	(-45.24, -22.47, 44.89)
1:156834527	rs201509045	V>M	A:99	(-47.39, -18.96, 47.67)
1:156834533	COSM1663163 COSM1663164	S>G	A:101	(-50.57, -24.14, 48.49)
1:156834534		S>N	A:101	(-50.57, -24.14, 48.49)
1:156834537	rs374170641	G>D	A:102	(-49.96, -27.52, 50.15)
1:156834542		R>C	A:104	(-46.03, -31.31, 54.32)
1:156834543	rs578095133 COSM3689057 COSM3689058	R>H	A:104	(-46.03, -31.31, 54.32)
1:156834548		V>M	A:106	(-40.04, -30.37, 47.92)
1:156834552	rs540521894 COSM20674 COSM1334979	A>V	A:107	(-38.42, -33.49, 46.15)
1:156834558	rs141592864	D>G	A:109	(-35.58, -33.32, 41.69)
1:156834573	rs202161010	T>S	A:114	(-34.92, -24.95, 36.52)
1:156834579		R>Q	A:116	(-29.53, -19.69, 35.37)
1:156834587		R>C	A:119	(-35.76, -13.72, 42.23)
1:156834588	COSM3475481 COSM48608 COSM3475482	R>H	A:119	(-35.76, -13.72, 42.23)
1:156836719	rs539589077	A>V	A:126	(-47.39, -26.69, 54.15)
1:156836736		W>R	A:132	(-28.17, -30.28, 50.67)
1:156836743		T>N	A:134	(-33.70, -28.45, 47.08)
1:156836748	rs576386597	Q>K	A:136	(-27.76, -28.15, 43.83)
1:156836749		Q>R	A:136	(-27.76, -28.15, 43.83)
1:156836750		Q>H	A:136	(-27.76, -28.15, 43.83)
1:156836766	rs370483210	E>K	A:142	(-34.94, -13.72, 46.03)
1:156837904	rs41267427	S>L	A:146	(-42.91, -18.28, 54.75)
1:156837913	rs144609655	P>H	A:149	(-44.76, -25.13, 59.09)
1:156837915		L>V	A:150	(-40.58, -24.20, 59.03)
1:156837919		H>R	A:151	(-39.44, -29.33, 62.82)
1:156837936	rs141629165	R>C	A:157	(-26.60, -25.08, 60.10)
1:156837948		R>C	A:161	(-24.12, -21.58, 56.92)
1:156837949	rs150271893	R>H	A:161	(-24.12, -21.58, 56.92)
1:156837951		W>R	A:162	(-28.61, -20.01, 52.13)
1:156837960		E>K	A:165	(-23.19, -16.76, 55.21)
1:156837962		E>D	A:165	(-23.19, -16.76, 55.21)
1:156837967		L>R	A:167	(-26.29, -15.73, 51.12)
1:156837970		G>V	A:168	(-30.76, -15.49, 49.96)
1:156837972	rs367836863 COSM3475485 COSM3475486	G>R	A:169	(-32.47, -13.58, 51.58)
1:156837976	rs201503610	V>A	A:170	(-33.03, -15.40, 54.62)
1:156837999		H>D	A:178	(-44.07, -26.30, 63.87)
1:156838011		P>S	A:182	(-39.21, -20.55, 67.70)
1:156838014	rs563804525	L>V	A:183	(-35.76, -18.45, 65.86)
1:156838024	rs371409149	M>T	A:186	(-30.96, -24.07, 66.34)
1:156838025		M>I	A:186	(-30.96, -24.07, 66.34)
1:156838026		P>S	A:187	(-29.69, -25.97, 68.45)
1:156838030	rs531080009	N>S	A:188	(-25.26, -24.74, 66.26)
1:156838032	rs200167354	A>T	A:189	(-23.01, -28.15, 67.60)
1:156838037	rs138608619	S>R	A:190	(-25.67, -31.10, 67.56)
1:156838306	rs552776147	T>M	A:195	(-15.73, -37.23, 59.53)
1:156838324	rs146201511	P>H	A:201	(-0.69, -47.36, 51.76)
1:156838333	rs148324672	S>L	A:204	(6.36, -47.25, 49.62)
1:156838339		D>V	A:206	(7.28, -49.24, 43.87)
1:156838353	rs201192875	V>M	A:211	(-2.73, -49.09, 45.73)
1:156838360	COSM1334980 COSM1334981 CM990975	L>P	A:213	(-7.58, -46.95, 49.23)
1:156838362	rs372041586	R>W	A:214	(-11.39, -49.24, 52.70)
1:156838363	rs200132482	R>Q	A:214	(-11.39, -49.24, 52.70)
1:156838381	rs540751200 COSM4140875 COSM4140876	R>Q	A:220	(-24.86, -39.47, 64.93)
1:156838398		G>S	A:226	(-18.41, -41.85, 46.44)
1:156838432	rs55909005	T>M	A:237	(-10.01, -48.80, 38.84)
1:156841425		G>V	A:243	(-20.46, -49.42, 51.81)
1:156841484	rs201509717	V>M	A:263	(-7.94, -39.89, 44.92)
1:156841505	rs145222195	D>N	A:270	(-29.29, -34.68, 57.38)
1:156841508		V>L	A:271	(-27.18, -31.07, 56.39)
1:156841514	rs151334385	R>W	A:273	(-20.75, -33.18, 49.25)
1:156841515	rs200305545 COSM4023447 COSM4023448	R>Q	A:273	(-20.75, -33.18, 49.25)
1:156841521	rs138533001	E>A	A:275	(-15.08, -33.46, 48.77)
1:156841539	rs547972574	N>T	A:281	(3.68, -40.78, 45.67)
1:156841541		V>I	A:282	(4.24, -43.79, 42.23)
1:156843428	rs141483265	P>L	A:285	(13.62, -43.55, 37.57)
1:156843439	rs137979116	Q>K	A:289	(17.09, -32.06, 30.05)
1:156843449		T>M	A:292	(22.17, -24.03, 25.60)
1:156843452	rs567093941	A>V	A:293	(23.52, -21.07, 27.96)
1:156843454		V>L	A:294	(20.80, -18.05, 28.48)
1:156843473		C>Y	A:300	(20.84, -19.60, 32.56)
1:156843493		G>R	A:307	(11.43, -38.08, 39.57)
1:156843514	rs137994522	R>C	A:314	(26.38, -33.43, 42.55)
1:156843523		F>L	A:317	(33.58, -25.97, 36.39)
1:156843527	rs532851293	N>S	A:318	(35.71, -28.74, 34.49)
1:156843535	rs369367198 COSM1259646 COSM1259647	V>M	A:321	(32.64, -30.01, 43.23)
1:156843542		N>S	A:323	(30.92, -25.03, 45.91)
1:156843544	COSM897410 COSM897411	E>K	A:324	(25.70, -23.55, 45.23)
1:156843548		T>N	A:325	(27.70, -18.94, 45.78)
1:156843562		T>A	A:330	(20.47, -24.03, 41.87)
1:156843568		F>I	A:332	(14.34, -25.60, 41.46)
1:156843595	rs139875058	V>M	A:341	(8.75, -32.16, 35.95)
1:156843613	rs561243137 COSM1217989 COSM1217990	R>C	A:347	(20.38, -17.46, 38.71)
1:156843620	rs528547348	N>S	A:349	(25.65, -12.70, 39.12)
1:156843621	rs370518146	N>K	A:349	(25.65, -12.70, 39.12)
1:156843634	rs201035170	V>I	A:354	(36.78, -17.74, 35.24)
1:156843653	rs371498291	T>M	A:360	(27.80, -31.68, 35.30)
1:156843670		P>S	A:366	(16.70, -44.13, 45.52)
1:156843671		P>R	A:366	(16.70, -44.13, 45.52)
1:156843674		F>S	A:367	(15.50, -45.92, 41.55)
1:156843699	COSM48611	M>I	A:375	(30.54, -26.52, 27.24)
1:156843700	rs551687143	A>P	A:376	(29.91, -22.64, 28.91)
1:156843713	rs140644885	D>G	A:380	(36.26, -14.13, 25.45)
1:156843716		N>S	A:381	(40.26, -15.79, 27.95)
1:156843718	rs569895276	P>S	A:382	(42.87, -12.30, 27.52)
1:156843719		P>H	A:382	(42.87, -12.30, 27.52)

2IFG.A | NTRK1.

2IFG.A | NTRK1

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
1:156834543	COSM3689058	R>H	A:104	(-46.03, -31.31, 54.32)
1:156834552	COSM1334979	A>V	A:107	(-38.42, -33.49, 46.15)
1:156843535	COSM1259646	V>M	A:321	(32.64, -30.01, 43.23)
1:156843581	COSM463173	A>E	A:336	(3.48, -27.77, 38.25)
1:156843583	COSM1688781	A>T	A:337	(0.21, -29.02, 38.40)
1:156843593	COSM3475492	T>I	A:340	(7.00, -34.98, 38.84)
1:156843599	COSM313388	R>Q	A:342	(10.93, -28.98, 39.52)
1:156843698	COSM1559917	M>T	A:375	(30.54, -26.52, 27.24)