1OLZ.B | SEMA4D

General Structure Information

PDB ID	1olz
HGNC Gene Label(s)	SEMA4D
Structure Name	the ligand-binding face of the semaphorins revealed by the high resolution crystal structure of sema4d
Resolution	2.0Å
Reference	AUTH C.A.LOVE,K.HARLOS,N.MAVADDAT,S.J.DAVIS,D.I.STUART,AUTH 2 E.Y.JONES,R.M.ESNOUFTITL THE LIGAND-BINDING FACE OF THE SEMAPHORINSTITL 2 REVEALED BY THE HIGH-RESOLUTION CRYSTAL STRUCTURETITL 3 OF SEMA4DREF NAT.STRUCT.BIOL. V. 10 843 2003REFN ISSN 1072-8368PMID 12958590DOI 10.1038/NSB977

Variant Set Distributions

ExAC Variants

Number Of Residues	622
Number Of SNVs	171
Number Of Permutations	86741
Optimal Distance Threshold	7.0
K Statistic	0.011
p-value	0.99

COSMIC

Number Of Residues	622
Number Of SNVs	10
Number Of Permutations	10610
Optimal Distance Threshold	19.0
K Statistic	0.267
p-value	0.483

Ripley’s K Analysis Plots

ExACCOSMIC

Variant Set Comparisons

Cosmic vs. ExAC

Number Of ExAC SNVs	171
Number Of COSMIC SNVs	12
Optimal Distance Threshold	51.0
K Statistic	-0.113
p-value	0.98

Pathogenic Proximity Analysis

COSMIC PathProx Analysis

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
9:92020298		A>V	B:4	(14.92, 2.25, 8.10)
9:92020296		P>S	B:5	(18.09, 1.12, 8.47)
9:92020291	rs150990736	I>M	B:6	(19.46, -3.26, 8.05)
9:92020293		I>V	B:6	(19.46, -3.26, 8.05)
9:92020290	rs142599830	P>T	B:7	(19.42, -4.49, 11.56)
9:92020280	rs141243393	T>I	B:10	(22.73, -9.89, 13.94)
9:92020274	rs147786200	E>G	B:12	(22.49, -15.30, 16.42)
9:92017914	rs576002602	F>L	B:21	(9.15, -19.91, 32.35)
9:92017898		I>T	B:26	(1.71, -24.86, 29.80)
9:92017895		Y>C	B:27	(1.82, -24.66, 25.26)
9:92017892		N>S	B:28	(-0.69, -19.83, 25.03)
9:92017884		A>T	B:31	(0.22, -12.42, 30.48)
9:92017869		E>K	B:36	(3.27, -4.51, 43.48)
9:92017863		K>E	B:38	(7.34, -8.32, 45.60)
9:92017841		A>G	B:45	(-1.12, -18.88, 30.51)
9:92017838		R>Q	B:46	(-3.39, -22.98, 27.12)
9:92017839		R>G	B:46	(-3.39, -22.98, 27.12)
9:92017832		A>V	B:48	(-1.76, -20.88, 34.09)
9:92017829		V>A	B:49	(-0.68, -18.26, 36.95)
9:92017815	rs62620228	A>T	B:54	(12.64, -10.86, 37.50)
9:92017811		L>P	B:55	(16.44, -10.83, 38.44)
9:92017791		H>Y	B:62	(4.82, -19.52, 43.64)
9:92014247	rs549593310	W>R	B:66	(-8.94, -21.02, 36.29)
9:92014217		C>R	B:76	(-17.49, -26.23, 24.41)
9:92014192		Q>R	B:84	(-8.19, -29.66, 21.02)
9:92011741		L>F	B:88	(-8.96, -24.55, 26.84)
9:92011737	COSM753911	N>S	B:89	(-8.74, -20.96, 31.08)
9:92011728		R>Q	B:92	(-6.84, -13.41, 27.81)
9:92011708	COSM3908776	A>T	B:99	(-0.42, -6.86, 48.02)
9:92011693		V>M	B:104	(-7.48, -13.54, 37.32)
9:92011680		N>S	B:108	(-13.69, -21.00, 31.27)
9:92011668		P>L	B:112	(-16.34, -15.89, 30.57)
9:92008566	rs201159484	L>S	B:119	(-0.07, -13.45, 45.93)
9:92008531		G>S	B:131	(-16.74, -12.25, 32.76)
9:92008486	COSM1166849	V>I	B:146	(-6.88, -0.87, 33.16)
9:92007445		E>G	B:151	(-13.01, -0.44, 39.58)
9:92007443		L>I	B:152	(-11.49, -3.81, 35.28)
9:92007436		S>L	B:154	(-12.79, -3.63, 29.63)
9:92007427	COSM1265184	S>L	B:157	(-16.22, -9.06, 23.18)
9:92007380		H>D	B:173	(-20.43, 1.94, 42.63)
9:92007377		S>G	B:174	(-21.42, 3.08, 38.87)
9:92007353		I>V	B:182	(-22.00, 1.71, 14.45)
9:92006319	rs377565599	V>M	B:191	(-4.60, -2.46, 21.31)
9:92006307	COSM198276	V>M	B:195	(-4.83, 5.71, 33.50)
9:92006300	rs138867489	R>Q	B:197	(-3.90, 8.92, 37.40)
9:92006301		R>G	B:197	(-3.90, 8.92, 37.40)
9:92006246		T>M	B:215	(-8.57, -0.76, 14.92)
9:92006215		F>L	B:225	(-11.59, -1.92, 0.05)
9:92006208		L>M	B:228	(-9.51, -0.29, 8.98)
9:92006189	rs371098071	R>K	B:234	(-11.96, 10.59, 26.65)
9:92006180		K>T	B:237	(-11.93, 7.99, 37.46)
9:92003950		G>S	B:242	(-27.18, 9.14, 33.48)
9:92003940		T>I	B:245	(-30.08, 10.19, 29.14)
9:92003934		Q>R	B:247	(-30.06, 5.45, 31.54)
9:92003904	rs138067294	R>Q	B:257	(-9.49, 10.51, 12.89)
9:92003892	rs150351780	S>F	B:261	(1.30, 9.35, 7.83)
9:92003890		R>W	B:262	(6.42, 9.29, 5.02)
9:92003877		G>A	B:266	(1.73, 7.40, 0.40)
9:92003878	COSM1110989	G>S	B:266	(1.73, 7.40, 0.40)
9:92003865		N>S	B:270	(-4.87, 1.86, 8.63)
9:92003860	rs371915585	L>V	B:272	(-3.15, 0.17, 16.28)
9:92003856	rs141385327	R>Q	B:273	(-0.88, -4.33, 14.84)
9:92003857		R>W	B:273	(-0.88, -4.33, 14.84)
9:92003851		V>I	B:275	(0.25, 1.54, 22.70)
9:92003845		V>M	B:277	(2.81, 5.23, 28.09)
9:92003839		R>G	B:279	(4.07, 7.57, 32.18)
9:92003832	rs201242261 COSM3413805	P>L	B:281	(10.53, 11.37, 35.94)
9:92003829	rs62638728	G>D	B:282	(11.30, 14.34, 33.10)
9:92003830	rs565206443	G>S	B:282	(11.30, 14.34, 33.10)
9:92003810		F>L	B:288	(0.42, 8.32, 24.04)
9:92003805	rs373564317	A>V	B:290	(2.48, 3.77, 18.32)
9:92003793	rs147822490	P>L	B:294	(-0.34, -1.44, 6.51)
9:92003794	rs370439510	P>A	B:294	(-0.34, -1.44, 6.51)
9:92003789		Q>H	B:295	(-5.94, -2.05, 5.22)
9:92003700		V>M	B:299	(4.51, -6.10, 1.38)
9:92003696		G>V	B:300	(5.80, -5.43, 5.06)
9:92003697		G>W	B:300	(5.80, -5.43, 5.06)
9:92003690	rs372587621	S>L	B:302	(6.14, -1.29, 9.99)
9:92003688		A>T	B:303	(5.27, 2.12, 11.97)
9:92003685		V>M	B:304	(6.73, 4.01, 15.21)
9:92003679	rs11526468	A>T	B:306	(4.77, 9.87, 18.51)
9:92003658	COSM1463514	E>K	B:313	(-5.75, 16.70, 26.27)
9:92003653	rs150937324	E>D	B:314	(-6.92, 20.88, 21.90)
9:92003643		H>Y	B:318	(-10.95, 23.10, 22.77)
9:92003640	rs142492709	G>R	B:319	(-13.14, 20.25, 19.00)
9:92003628		Q>E	B:323	(-23.46, 15.47, 12.21)
9:92003625		S>G	B:324	(-24.70, 11.61, 11.05)
9:92003618	rs374906237	T>I	B:326	(-29.72, 10.44, 6.43)
9:92003601		T>S	B:332	(-25.10, 7.21, 6.84)
9:92003585		Y>C	B:337	(-22.03, 20.17, 14.52)
9:92003576	rs148588269	P>L	B:340	(-24.95, 24.49, 18.01)
9:92003570		P>H	B:342	(-24.23, 21.59, 23.95)
9:92003564		P>L	B:344	(-22.37, 21.37, 29.45)
9:92003565		P>S	B:344	(-22.37, 21.37, 29.45)
9:92003561	rs369287352	R>Q	B:345	(-17.41, 20.02, 25.12)
9:92003562		R>W	B:345	(-17.41, 20.02, 25.12)
9:92003552		A>V	B:348	(-16.76, 16.39, 29.55)
9:92003553		A>T	B:348	(-16.76, 16.39, 29.55)
9:92002520		I>V	B:350	(-17.48, 16.83, 36.21)
9:92002511		E>K	B:353	(-15.85, 24.53, 33.16)
9:92002508		A>S	B:354	(-19.33, 22.22, 35.76)
9:92002504	rs377092543	R>Q	B:355	(-17.88, 20.89, 40.11)
9:92002505	rs374901596	R>W	B:355	(-17.88, 20.89, 40.11)
9:92002499	rs564046242 COSM1110988	A>T	B:357	(-22.84, 25.12, 37.03)
9:92002495		N>S	B:358	(-24.13, 24.12, 40.30)
9:92002486		S>T	B:361	(-22.57, 14.29, 38.65)
9:92002472		P>S	B:366	(-27.86, 18.56, 30.87)
9:92002462	COSM3849052	T>M	B:369	(-25.29, 17.38, 27.07)
9:92002441		H>R	B:376	(-22.61, 13.97, 18.17)
9:92002439		P>S	B:377	(-19.13, 9.93, 19.46)
9:92002423	rs143896387	S>L	B:382	(-6.86, 14.19, 13.45)
9:92002421		V>I	B:383	(-4.69, 12.66, 16.85)
9:92002415		P>T	B:385	(2.03, 12.79, 14.77)
9:92002411		I>T	B:386	(5.61, 14.38, 17.52)
9:92002412	rs200806630	I>V	B:386	(5.61, 14.38, 17.52)
9:92002404	rs368013568	N>K	B:388	(2.89, 15.56, 11.15)
9:92002381	rs140150679	D>V	B:396	(10.91, -6.32, 4.46)
9:92002382	rs374159682	D>H	B:396	(10.91, -6.32, 4.46)
9:92002365		Q>H	B:401	(4.28, -5.58, 20.89)
9:92002361	rs542114524 COSM3908770	V>M	B:403	(8.82, -1.14, 24.71)
9:92002351	COSM1110987	R>Q	B:406	(13.22, 9.21, 27.96)
9:92002352		R>W	B:406	(13.22, 9.21, 27.96)
9:92002349	rs556121720	T>A	B:407	(18.52, 6.64, 28.01)
9:92002324	rs142880678	Y>C	B:415	(19.51, 9.13, 22.78)
9:92002309		V>A	B:420	(10.45, -3.29, 18.23)
9:92002310		V>F	B:420	(10.45, -3.29, 18.23)
9:92001394	rs369861571	R>Q	B:424	(9.82, -15.47, 12.22)
9:92001371		S>G	B:432	(16.40, 8.83, 16.80)
9:92001365		E>K	B:434	(22.40, 12.17, 13.72)
9:92001358		A>G	B:436	(18.01, 9.13, 11.33)
9:92001359		A>T	B:436	(18.01, 9.13, 11.33)
9:92001350		I>V	B:439	(18.28, -0.43, 13.78)
9:92001344	rs139590784	E>K	B:441	(20.75, -4.63, 18.54)
9:92001334	COSM247243	Q>R	B:444	(15.80, -14.54, 17.40)
9:92001320	rs201097053	F>L	B:449	(11.70, -18.44, 14.03)
9:92001316		E>G	B:450	(6.32, -18.45, 17.97)
9:92001307		Q>L	B:453	(1.80, -12.77, 21.69)
9:91996255	rs141391829	R>G	B:464	(16.24, -1.67, 33.18)
9:91996245		Y>C	B:467	(10.59, -9.25, 31.05)
9:91996230		S>L	B:472	(6.66, -20.95, 23.35)
9:91996218		Q>R	B:476	(15.01, -12.33, 30.81)
9:91996212		P>L	B:478	(19.23, -7.54, 28.21)
9:91996206		A>D	B:480	(22.22, -4.46, 26.38)
9:91996188		G>D	B:486	(35.63, -6.33, 22.05)
9:91996189		G>S	B:486	(35.63, -6.33, 22.05)
9:91996183	rs143625831	C>R	B:488	(36.64, 0.65, 21.58)
9:91996175		D>E	B:490	(33.47, -2.91, 18.03)
9:91996164	rs75298730	A>V	B:494	(27.29, 0.75, 17.97)
9:91996161		R>Q	B:495	(26.39, 4.03, 16.37)
9:91996137		P>L	B:503	(39.56, 2.25, 29.63)
9:91996131		T>R	B:505	(38.47, -2.99, 32.31)
9:91996128	COSM3358379	A>V	B:506	(39.25, -3.52, 28.51)
9:91996120	rs145920058	V>M	B:509	(30.50, -1.22, 29.94)
9:91996114	rs62638723	L>V	B:511	(26.83, 3.97, 31.02)
9:91996111		H>Y	B:512	(23.74, 3.90, 33.66)
9:91996107		Q>P	B:513	(24.79, -1.56, 34.97)
9:91996105		T>S	B:514	(29.90, 0.49, 35.52)
9:91996102		E>K	B:515	(32.11, -0.77, 38.60)
9:91996095		P>R	B:517	(35.45, 5.37, 36.36)
9:91996096	rs199707488	P>S	B:517	(35.45, 5.37, 36.36)
9:91996011	rs370952381	G>D	B:520	(36.67, 7.58, 31.44)
9:91996006		I>L	B:522	(35.22, 5.87, 25.67)
9:91995999		E>G	B:524	(31.79, 9.11, 20.82)
9:91996000		E>Q	B:524	(31.79, 9.11, 20.82)
9:91995994	rs376445150	S>C	B:526	(29.36, 9.96, 16.14)
9:91995991		G>S	B:527	(31.14, 6.88, 15.79)
9:91995979		V>L	B:531	(39.39, 8.42, 21.22)
9:91995972	rs567628518	P>L	B:533	(42.20, 2.84, 23.38)
9:91994529		S>T	B:539	(42.44, -10.63, 14.96)
9:91994530		S>R	B:539	(42.44, -10.63, 14.96)
9:91994526		Y>C	B:540	(48.38, -11.64, 14.44)
9:91994523		R>Q	B:541	(45.51, -15.80, 13.44)
9:91994524	rs147086169	R>W	B:541	(45.51, -15.80, 13.44)
9:91994517		H>R	B:543	(48.63, -18.26, 8.28)
9:91994508	COSM1110983	K>T	B:546	(52.87, -26.78, 1.11)
9:91994493	rs143261735	A>V	B:551	(44.29, -20.33, 1.66)
9:91994479		S>P	B:556	(35.11, -11.57, 11.28)
9:91994475		Q>P	B:557	(32.30, -8.30, 10.06)
9:91994457		R>Q	B:563	(31.58, -3.36, 1.47)
9:91994435		N>K	B:570	(50.48, -0.78, 0.74)
9:91994433	rs45464494	G>D	B:571	(47.75, -2.21, -0.83)
9:91994431		V>L	B:572	(44.07, -1.99, -1.96)
9:91994426		L>F	B:573	(43.56, -6.90, -2.63)
9:91994419	rs536075771	E>K	B:576	(39.76, -9.71, -9.50)
9:91994397	rs369241785	M>T	B:583	(34.42, -18.30, 0.79)
9:91994370		N>T	B:592	(48.50, -21.46, -6.84)
9:91994358		G>E	B:596	(54.55, -13.18, -3.56)
9:91994346		V>A	B:600	(50.55, -9.00, 5.90)
9:91994322		R>T	B:608	(29.38, 4.49, 4.92)
9:91994298		Q>R	B:616	(37.43, -1.65, 11.89)
9:91994295		V>A	B:617	(41.58, -3.43, 11.10)
9:91994290	rs371991421	A>T	B:619	(41.82, -8.64, 10.06)
9:91994281	COSM3395925	V>I	B:622	(50.97, -12.87, 9.00)

1OLZ.B | SEMA4D.

1OLZ.B | SEMA4D

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
9:92017824	COSM4408635	A>T	B:51	(5.72, -16.87, 39.82)
9:92017815	COSM4806538	A>T	B:54	(12.64, -10.86, 37.50)
9:92011678	COSM198278	A>T	B:109	(-14.74, -22.62, 27.92)
9:92008486	COSM1166849	V>I	B:146	(-6.88, -0.87, 33.16)
9:92007428	COSM3221629	S>T	B:157	(-16.22, -9.06, 23.18)
9:92006307	COSM198276	V>M	B:195	(-4.83, 5.71, 33.50)
9:92006198	COSM198274	R>Q	B:231	(-10.61, 5.64, 16.08)
9:92003658	COSM4646859	E>K	B:313	(-5.75, 16.70, 26.27)
9:92003589	COSM198271	R>C	B:336	(-16.26, 19.80, 10.79)
9:92002518	COSM4932930	I>M	B:350	(-17.48, 16.83, 36.21)
9:92002479	COSM4724741	L>F	B:363	(-26.28, 11.65, 37.55)
9:91994364	COSM1315011	S>L	B:594	(53.44, -18.43, -4.63)
9:91994281	COSM3395925	V>I	B:622	(50.97, -12.87, 9.00)