1XDV.B | SOS1 – ASTRID

1XDV.B | SOS1

General Structure Information

PDB ID	1xdv
HGNC Gene Label(s)	SOS1
Structure Name	experimentally phased structure of human the son of sevenless protein at 4.1 ang.
Resolution	4.1Å
Reference	AUTH H.SONDERMANN,S.M.SOISSON,S.BOYKEVISCH,S.S.YANG,AUTH 2 D.BAR-SAGI,J.KURIYANTITL STRUCTURAL ANALYSIS OF AUTOINHIBITION IN THE RASTITL 2 ACTIVATOR SON OF SEVENLESS.REF CELL(CAMBRIDGE,MASS.) V. 119 393 2004REFN ISSN 0092-8674PMID 15507210DOI 10.1016/J.CELL.2004.10.005

Variant Set Distributions

ExAC Variants

Number Of Residues	759
Number Of SNVs	121
Number Of Permutations	80017
Optimal Distance Threshold	43.0
K Statistic	0.436
p-value	0.267

ClinVar

Number Of Residues	759
Number Of SNVs	20
Number Of Permutations	25221
Optimal Distance Threshold	6.0
K Statistic	0.037
p-value	0.017

COSMIC

Number Of Residues	759
Number Of SNVs	9
Number Of Permutations	14212
Optimal Distance Threshold	52.0
K Statistic	0.722
p-value	0.611

Ripley’s K Analysis Plots

ExACClinVarCOSMIC

Variant Set Comparisons

ClinVar vs. ExAC

Number Of ExAC SNVs	121
Number Of ClinVar SNVs	19
Optimal Distance Threshold	13.0
K Statistic	0.091
p-value	0.028

Cosmic vs. ExAC

Number Of ExAC SNVs	121
Number Of COSMIC SNVs	9
Optimal Distance Threshold	52.0
K Statistic	0.17
p-value	0.421

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
2:39281876	rs143007609	T>S	B:200	(68.54, 82.96, 13.91)
2:39281856		A>T	B:207	(58.55, 79.72, 13.62)
2:39281837	rs374761537	R>Q	B:213	(52.28, 75.13, 18.53)
2:39281832	COSM1193505	Y>H	B:215	(49.73, 70.94, 10.37)
2:39281829		I>L	B:216	(48.52, 70.23, 15.20)
2:39281808		I>V	B:223	(40.47, 64.37, 12.44)
2:39281783		V>A	B:231	(33.75, 57.33, 10.72)
2:39281777	rs144934321	N>S	B:233	(27.33, 56.90, 8.38)
2:39281760		A>T	B:239	(36.60, 52.47, 4.85)
2:39278416		I>V	B:245	(38.11, 61.66, 1.32)
2:39278412		F>Y	B:246	(39.51, 62.29, 5.05)
2:39278406		R>H	B:248	(46.97, 57.66, 6.07)
2:39278400	rs139290271	V>A	B:250	(45.39, 59.87, 11.58)
2:39278394	rs142094234	I>T	B:252	(50.07, 63.16, 9.21)
2:39278376		K>M	B:258	(54.94, 62.72, 18.76)
2:39278364	COSM95260	H>R	B:262	(60.28, 64.74, 20.68)
2:39278349		V>A	B:267	(63.53, 74.06, 24.07)
2:39278314	rs188055807	V>I	B:279	(66.35, 70.49, 16.63)
2:39262616		S>L	B:297	(50.99, 58.33, 0.57)
2:39262607		R>Q	B:300	(50.87, 58.94, -4.20)
2:39262608		R>G	B:300	(50.87, 58.94, -4.20)
2:39262577	rs143481916	R>H	B:310	(37.04, 60.19, -5.31)
2:39262571	rs139274919	L>R	B:312	(31.90, 65.84, -5.64)
2:39262564		Q>H	B:314	(31.24, 59.87, -1.61)
2:39262560		S>T	B:316	(26.18, 62.98, -4.64)
2:39262448	COSM3407858	I>V	B:327	(25.80, 66.96, 11.09)
2:39262442		E>K	B:329	(23.30, 75.42, 10.52)
2:39262428		E>D	B:333	(27.76, 74.10, 3.00)
2:39262426		A>V	B:334	(32.24, 73.06, 4.55)
2:39262427		A>T	B:334	(32.24, 73.06, 4.55)
2:39262420		Q>R	B:336	(31.00, 70.94, -1.49)
2:39262417		Y>C	B:337	(31.86, 74.46, -1.69)
2:39262409	rs190222208	P>S	B:340	(38.85, 70.61, -0.30)
2:39262376		L>F	B:351	(56.80, 70.89, 0.53)
2:39251178	COSM3426438	S>C	B:392	(54.84, 69.02, -10.95)
2:39250307		K>M	B:421	(50.90, 95.26, -2.65)
2:39250302		N>D	B:423	(49.60, 100.82, 0.66)
2:39250298		E>G	B:424	(51.16, 100.13, -4.26)
2:39250299		E>K	B:424	(51.16, 100.13, -4.26)
2:39250283		I>T	B:429	(41.46, 101.47, -5.85)
2:39250277		G>V	B:431	(36.69, 105.35, -4.47)
2:39250231		M>I	B:446	(42.90, 85.60, -3.84)
2:39250182	COSM1020878	L>V	B:463	(41.13, 88.15, -1.00)
2:39250148		N>S	B:474	(38.51, 101.97, -15.68)
2:39250079	rs371314838 CM105249	R>Q	B:497	(34.22, 89.44, 11.08)
2:39250073		V>A	B:499	(28.74, 82.80, 5.71)
2:39250046		N>S	B:508	(20.49, 82.17, -14.54)
2:39250047		N>H	B:508	(20.49, 82.17, -14.54)
2:39250041	rs201404055	Y>N	B:510	(24.23, 80.80, -11.47)
2:39250037		K>R	B:511	(29.15, 78.79, -14.55)
2:39250029	rs561772850	F>L	B:514	(30.81, 81.90, -4.74)
2:39250011		D>N	B:520	(22.90, 93.34, 8.25)
2:39250008		E>K	B:521	(24.63, 93.08, 4.37)
2:39250005		N>H	B:522	(22.24, 91.85, 0.38)
2:39250000		S>R	B:523	(22.98, 87.94, -0.70)
2:39249995	rs146722878	I>T	B:525	(25.67, 85.24, -6.19)
2:39249965	COSM1531955	N>I	B:535	(38.02, 75.11, -6.87)
2:39249943		I>M	B:542	(35.97, 78.03, 3.21)
2:39249945		I>V	B:542	(35.97, 78.03, 3.21)
2:39249935		Q>R	B:545	(34.08, 81.00, 7.29)
2:39249929	rs149775695	R>Q	B:547	(41.25, 81.78, 11.41)
2:39249864	rs200786705	L>V	B:569	(44.50, 62.75, 40.77)
2:39249849		V>I	B:574	(52.79, 58.15, 52.31)
2:39249819	COSM1020874	E>K	B:584	(53.39, 74.88, 56.85)
2:39249807		F>L	B:588	(55.93, 82.12, 46.21)
2:39249776		I>T	B:598	(58.03, 82.06, 36.38)
2:39249771	rs373139450	I>V	B:600	(60.08, 84.64, 42.37)
2:39249755		T>N	B:605	(60.95, 72.53, 52.17)
2:39249749		I>T	B:607	(60.75, 68.43, 49.47)
2:39249740		I>T	B:610	(63.69, 69.63, 44.68)
2:39249741		I>V	B:610	(63.69, 69.63, 44.68)
2:39249718		M>I	B:617	(52.79, 73.42, 35.28)
2:39249719		M>T	B:617	(52.79, 73.42, 35.28)
2:39241981	rs145443784	N>S	B:622	(66.81, 81.18, 35.54)
2:39241954		Y>F	B:631	(73.50, 72.55, 46.46)
2:39241915		I>T	B:644	(67.00, 64.14, 42.05)
2:39241119		P>L	B:651	(54.40, 56.59, 42.37)
2:39241014		Q>L	B:686	(60.77, 61.41, 34.47)
2:39240698		L>F	B:690	(67.14, 63.90, 33.49)
2:39240663		Y>C	B:702	(82.36, 71.74, 41.64)
2:39240646	rs140811086	A>T	B:708	(83.55, 59.16, 43.54)
2:39240630	rs483352826 COSM3581521	R>Q	B:713	(74.29, 57.86, 44.03)
2:39240628		M>V	B:714	(74.80, 60.19, 38.38)
2:39240612	rs200794965	G>A	B:719	(71.12, 53.44, 33.94)
2:39240610	rs367634525	T>A	B:720	(67.94, 53.33, 36.00)
2:39240607		V>I	B:721	(66.68, 55.36, 32.24)
2:39240603	rs142666652	R>K	B:722	(62.99, 53.58, 33.22)
2:39239460	rs574088829 COSM395978 CM070276	I>L	B:733	(73.64, 63.25, 30.25)
2:39239451		I>V	B:736	(78.56, 65.80, 29.39)
2:39239375		V>G	B:761	(106.67, 89.81, 22.82)
2:39239342		E>G	B:772	(119.79, 82.93, 34.25)
2:39239313		I>V	B:782	(104.85, 96.49, 28.26)
2:39239286	rs142004123	L>I	B:791	(98.91, 84.64, 35.32)
2:39239277		D>Y	B:794	(93.80, 82.42, 33.48)
2:39237799		E>D	B:812	(86.68, 74.30, 59.12)
2:39237746	rs397517158	N>S	B:830	(103.13, 86.54, 46.23)
2:39234332		C>Y	B:838	(111.92, 94.94, 45.07)
2:39234315		N>H	B:844	(120.95, 103.03, 45.86)
2:39234284	COSM1668859	R>Q	B:854	(110.74, 99.90, 35.52)
2:39234278		I>T	B:856	(104.34, 103.66, 38.66)
2:39234274		E>D	B:857	(106.10, 102.37, 33.96)
2:39234258	rs141501083	Q>K	B:863	(94.72, 101.38, 34.57)
2:39234255		E>Q	B:864	(96.67, 100.62, 29.17)
2:39234222		V>I	B:875	(97.83, 100.53, 45.25)
2:39234183		H>Y	B:888	(114.27, 110.73, 51.02)
2:39234175		F>L	B:890	(107.52, 108.19, 46.51)
2:39234173		E>G	B:891	(110.96, 114.16, 46.67)
2:39233618		E>G	B:909	(89.10, 107.22, 47.72)
2:39233616	rs369277679	D>H	B:910	(84.35, 107.05, 49.09)
2:39233606		K>R	B:913	(81.75, 105.80, 44.44)
2:39233580		I>V	B:922	(85.00, 99.03, 30.95)
2:39224560		Y>C	B:933	(82.45, 90.66, 43.35)
2:39224546	rs566328117	L>V	B:938	(79.91, 87.27, 54.06)
2:39224498		E>K	B:954	(60.21, 77.74, 59.27)
2:39224483		S>G	B:959	(65.64, 86.96, 48.19)
2:39224472		R>S	B:962	(66.72, 85.92, 43.69)
2:39224470		K>R	B:963	(70.85, 89.50, 46.81)
2:39224405		S>A	B:985	(106.01, 80.48, 28.70)
2:39224395		K>R	B:988	(103.47, 82.04, 32.86)
2:39224171		F>L	B:991	(106.05, 86.85, 37.27)
2:39224165		N>K	B:993	(107.85, 80.06, 40.34)
2:39224157	rs200747626 COSM1020871	P>L	B:996	(108.59, 86.67, 48.22)
2:39224148		N>S	B:999	(111.20, 79.42, 54.29)
2:39224112	rs8192671	N>S	B:1011	(113.12, 96.49, 60.17)
2:39224101		E>K	B:1015	(118.57, 99.78, 56.81)
2:39224086		N>H	B:1020	(113.21, 113.03, 60.46)
2:39224067		R>K	B:1026	(125.66, 108.24, 50.74)
2:39222507		L>I	B:1035	(118.63, 101.99, 35.98)

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
2:39278352	rs137852812	T>K	B:266	(64.81, 70.00, 23.30)
2:39278343	rs137852813	M>R	B:269	(66.15, 69.99, 28.73)
2:39262581	rs397517180	D>Y	B:309	(35.55, 64.32, -9.79)
2:39251221	rs397517146	T>A	B:378	(69.94, 62.23, 3.17)
2:39250298	rs730881042	E>G	B:424	(51.16, 100.13, -4.26)
2:39250299	rs730881041	E>K	B:424	(51.16, 100.13, -4.26)
2:39250275	rs267607080	W>R	B:432	(39.09, 102.72, -0.23)
2:39250272	rs397517147	E>K	B:433	(34.13, 103.48, 0.58)
2:39250267	rs730881048	G>K	B:434	(36.83, 103.91, 4.61)
2:39250269	rs397517148	G>R	B:434	(36.83, 103.91, 4.61)
2:39250259	rs397517150	I>S	B:437	(43.75, 97.87, 3.16)
2:39250247	rs727504295	C>Y	B:441	(44.06, 93.90, 6.70)
2:39250184	rs730881043	F>Y	B:462	(42.07, 93.26, -5.23)
2:39250157	rs397517151	C>S	B:471	(36.87, 96.43, -8.54)
2:39249925	rs730881045	S>R	B:548	(39.93, 79.40, 14.07)
2:39249927	rs397517149	S>R	B:548	(39.93, 79.40, 14.07)
2:39249923	rs730881046	T>K	B:549	(39.95, 75.29, 12.73)
2:39249920	rs397517153	L>P	B:550	(41.90, 76.06, 9.24)
2:39240663	rs757094189	Y>C	B:702	(82.36, 71.74, 41.64)
2:39240664	rs727505381	Y>H	B:702	(82.36, 71.74, 41.64)
2:39239474	rs397517156	K>I	B:728	(69.31, 58.25, 21.84)
2:39239460	rs574088829	I>F	B:733	(73.64, 63.25, 30.25)
2:39234309	rs397517159	E>K	B:846	(119.97, 106.03, 41.47)
2:39224122	rs397517163	Y>H	B:1008	(113.37, 91.90, 55.93)

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
2:39281778	COSM95261	N>Y	B:233	(27.33, 56.90, 8.38)
2:39278343	COSM1690495	M>K	B:269	(66.15, 69.99, 28.73)
2:39250247	COSM3372774	C>Y	B:441	(44.06, 93.90, 6.70)
2:39249841	COSM1614841	R>S	B:576	(56.20, 61.67, 45.52)
2:39249723	COSM442890	H>Y	B:616	(53.76, 69.81, 36.74)
2:39239450	COSM1668860	I>R	B:736	(78.56, 65.80, 29.39)
2:39239292	COSM1752548	T>P	B:789	(97.06, 90.29, 32.83)
2:39234309	COSM419169	E>K	B:846	(119.97, 106.03, 41.47)
2:39224440	COSM3581519	Q>L	B:973	(79.20, 88.12, 32.02)

1XDV.B | SOS1.

1XDV.B | SOS1

General Structure Information

Variant Set Distributions

Ripley’s K Analysis Plots

Variant Set Comparisons

Mapped Variants

[+] ExAC Missense Variants

[+] ClinVar Missense Variants

[+] COSMIC Missense Variants