4ELJ.A | RB1 – ASTRID

4ELJ.A | RB1

General Structure Information

PDB ID	4elj
HGNC Gene Label(s)	RB1
Structure Name	crystal structure of the inactive retinoblastoma protein phosphorylated at t373
Resolution	2.7Å
Reference	AUTH J.R.BURKE,G.L.HURA,S.M.RUBINTITL STRUCTURES OF INACTIVE RETINOBLASTOMA PROTEIN REVEALTITL 2 MULTIPLE MECHANISMS FOR CELL CYCLE CONTROL.REF GENES DEV. V. 26 1156 2012REFN ISSN 0890-9369PMID 22569856DOI 10.1101/GAD.189837.112

Variant Set Distributions

ExAC Variants

Number Of Residues	588
Number Of SNVs	88
Number Of Permutations	22242
Optimal Distance Threshold	9.0
K Statistic	0.024
p-value	0.694

ClinVar

Number Of Residues	588
Number Of SNVs	12
Number Of Permutations	2901
Optimal Distance Threshold	11.0
K Statistic	0.167
p-value	0.001

COSMIC

Number Of Residues	588
Number Of SNVs	28
Number Of Permutations	8608
Optimal Distance Threshold	17.0
K Statistic	0.243
p-value	0.0

Ripley’s K Analysis Plots

ExACClinVarCOSMIC

Variant Set Comparisons

ClinVar vs. ExAC

Number Of ExAC SNVs	88
Number Of ClinVar SNVs	12
Optimal Distance Threshold	11.0
K Statistic	0.127
p-value	0.003

Cosmic vs. ExAC

Number Of ExAC SNVs	88
Number Of COSMIC SNVs	16
Optimal Distance Threshold	13.0
K Statistic	0.097
p-value	0.045

Pathogenic Proximity Analysis

ClinVar PathProx Analysis

COSMIC PathProx Analysis

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
13:48881441		P>T	A:55	(-21.69, -13.78, 76.06)
13:48881451	rs138574644	T>I	A:58	(-19.69, -17.14, 72.40)
13:48881453	rs184754468	A>P	A:59	(-23.49, -18.39, 71.59)
13:48881483		H>D	A:69	(-8.81, -21.07, 64.18)
13:48881484		H>R	A:69	(-8.81, -21.07, 64.18)
13:48881492	rs369833913 CM952102	E>K	A:72	(-10.29, -16.51, 67.69)
13:48881493		E>G	A:72	(-10.29, -16.51, 67.69)
13:48881496		R>T	A:73	(-10.05, -13.87, 61.21)
13:48881499		A>G	A:74	(-15.28, -13.03, 63.94)
13:48881523	COSM905 CM034896	S>L	A:82	(-16.50, -1.18, 66.27)
13:48881537	rs543611480	V>I	A:87	(-22.82, 1.31, 60.93)
13:48916765		W>R	A:99	(-22.20, -10.22, 67.23)
13:48916837	rs149800437	N>D	A:123	(-29.58, -17.70, 64.17)
13:48916840		I>V	A:124	(-28.89, -13.02, 62.25)
13:48919228		F>L	A:131	(-26.13, -10.42, 55.19)
13:48919246	rs3092902	E>D	A:137	(-21.40, -0.48, 55.24)
13:48919277		M>V	A:148	(-23.02, -12.12, 49.04)
13:48919281		S>L	A:149	(-22.36, -11.76, 44.60)
13:48919294		K>N	A:153	(-26.33, -13.27, 41.48)
13:48919299		Y>C	A:155	(-32.92, -14.43, 46.88)
13:48919320	COSM1367170 COSM1367169	F>Y	A:162	(-41.59, -19.87, 44.27)
13:48921987		Q>L	A:176	(-60.08, -26.37, 46.76)
13:48923132		S>T	A:194	(-43.06, -28.86, 40.71)
13:48923152	rs571823638	L>F	A:200	(-33.29, -31.71, 41.87)
13:48934158		V>I	A:205	(-29.09, -29.15, 33.49)
13:48934173	rs148992508	D>Y	A:210	(-27.23, -16.87, 37.29)
13:48934188		S>P	A:215	(-34.25, -22.03, 34.29)
13:48934189	COSM432451 COSM13412 COSM1477252 COSM1477251 CM034898	S>L	A:215	(-34.25, -22.03, 34.29)
13:48934219		Y>C	A:225	(-44.58, -34.81, 34.25)
13:48934228	COSM1236130 COSM1236129	K>R	A:228	(-49.83, -33.88, 31.35)
13:48934230		L>F	A:229	(-49.96, -36.20, 36.51)
13:48936962		I>V	A:244	(-58.69, -33.78, 27.03)
13:48936963	rs147754935	I>T	A:244	(-58.69, -33.78, 27.03)
13:48937082		N>D	A:284	(-39.34, -19.72, 21.48)
13:48939065		F>L	A:299	(-33.97, -35.38, 35.73)
13:48939088	rs183898408	T>I	A:307	(-41.77, -42.84, 39.73)
13:48939097	rs200844292 COSM327253 CM057985 CD030598	G>E	A:310	(-45.73, -40.52, 37.62)
13:48941631		V>D	A:314	(-42.50, -35.65, 47.45)
13:48941642		S>P	A:318	(-36.79, -33.39, 49.79)
13:48941648	rs121913300 COSM891 COSM1152653 CM941205	R>G	A:320	(-32.35, -37.07, 45.70)
13:48941649	COSM1367193 COSM1367192	R>Q	A:320	(-32.35, -37.07, 45.70)
13:48941654	COSM1367201 COSM317951 COSM1367200 CM071073	E>K	A:322	(-31.52, -31.98, 52.91)
13:48941655	rs142620145	E>G	A:322	(-31.52, -31.98, 52.91)
13:48941658	COSM1367204 COSM1367203	E>G	A:323	(-27.93, -34.65, 51.09)
13:48941669		K>E	A:327	(-22.68, -30.35, 49.29)
13:48941678		D>N	A:330	(-26.80, -22.70, 49.37)
13:48941685	COSM4170227	D>G	A:332	(-33.41, -24.59, 51.98)
13:48941714		T>S	A:342	(-34.99, -16.30, 55.32)
13:48947542	rs146897002	T>S	A:377	(-38.67, -8.58, 31.15)
13:48947569	rs564780653	M>V	A:386	(-37.35, -13.36, 17.40)
13:48947572	rs190689977	M>L	A:387	(-39.63, -8.70, 16.09)
13:48947573		M>T	A:387	(-39.63, -8.70, 16.09)
13:48947576	rs373623059 COSM1367214 COSM35887 COSM1367213	I>S	A:388	(-35.02, -7.72, 14.52)
13:48947587	rs181988132	A>T	A:392	(-33.15, -13.89, 8.54)
13:48947593		D>N	A:394	(-29.11, -19.67, 8.30)
13:48947617		S>P	A:402	(-24.16, -10.34, -5.32)
13:48951106		G>E	A:423	(-19.54, -22.47, 16.19)
13:48951109	COSM1562223 COSM1562222	Y>C	A:424	(-15.58, -26.09, 17.33)
13:48951118		K>T	A:427	(-21.84, -24.88, 19.89)
13:48951144	rs4151534	Q>K	A:436	(-21.59, -30.49, 28.31)
13:48953731	COSM1367226 COSM1367225	R>Q	A:445	(-29.01, -19.07, 22.27)
13:48953748	COSM176711 COSM1147221	R>C	A:451	(-31.24, -15.41, 11.79)
13:48953761		R>Q	A:455	(-30.65, -7.94, 8.97)
13:48954207	rs139960834	I>L	A:470	(-18.79, 1.05, -5.44)
13:48954342	COSM254915 COSM1629126 COSM1587097 COSM1629125	A>V	A:488	(-19.16, -10.44, 18.14)
13:48954354		E>V	A:492	(-23.16, -9.33, 23.13)
13:48954362		M>L	A:495	(-25.64, -13.85, 24.61)
13:48954366	rs560971404	A>G	A:496	(-27.91, -9.84, 26.15)
13:48954368		T>A	A:497	(-31.38, -10.63, 24.56)
13:48954375		S>N	A:499	(-29.26, -12.21, 29.84)
13:48955389	COSM3720556 COSM3720555	T>I	A:502	(-26.55, -5.27, 33.02)
13:48955457	COSM3469152 COSM3469151	A>T	A:525	(-11.51, -4.78, 22.38)
13:48955458	rs4151539	A>G	A:525	(-11.51, -4.78, 22.38)
13:48955501	rs371031574	E>D	A:539	(-30.04, -2.97, 12.66)
13:48955503		G>V	A:540	(-32.58, 0.13, 12.95)
13:48955547		H>Y	A:555	(-18.76, 3.18, 28.14)
13:48955551	COSM1367251 COSM1367250	R>Q	A:556	(-16.71, -3.01, 30.32)
13:48955565		L>F	A:561	(-11.18, -4.12, 28.10)
13:49027165		D>Y	A:578	(5.88, 10.83, 15.42)
13:49027169	COSM1367268 COSM1367267 CD062219 CD086245	R>Q	A:579	(5.57, 15.56, 14.40)
13:49030471		L>R	A:649	(-12.47, 8.96, 17.55)
13:49033827		Y>F	A:655	(-9.81, 12.84, 27.04)
13:49033829	rs142509759	R>W	A:656	(-18.14, 12.74, 26.53)
13:49033830	rs202031219	R>Q	A:656	(-18.14, 12.74, 26.53)
13:49033839	COSM35346 COSM1559421	Y>C	A:659	(-14.66, 16.52, 32.47)
13:49033844	rs137853294	R>W	A:661	(-16.78, 8.46, 34.73)
13:49033865	rs369755801	R>C	A:668	(-20.96, 13.60, 46.09)
13:49033866	rs551747882	R>H	A:668	(-20.96, 13.60, 46.09)
13:49033896	rs201046651	H>L	A:678	(-8.46, 23.35, 36.23)
13:49033941		E>G	A:693	(3.40, 2.05, 29.96)
13:49033954	rs3092903	D>E	A:697	(-3.46, -4.36, 32.58)
13:49037940		A>V	A:727	(-18.41, 8.52, 45.79)
13:49037948		D>H	A:730	(-22.69, 6.28, 44.38)
13:49039143	rs529366765	R>C	A:741	(-7.88, -6.93, 42.26)
13:49039162		E>A	A:747	(1.31, -11.41, 38.24)
13:49039163		E>D	A:747	(1.31, -11.41, 38.24)
13:49039194		S>A	A:758	(3.85, 2.84, 44.76)
13:49039195	COSM947803 COSM1587092	S>L	A:758	(3.85, 2.84, 44.76)
13:49039212	rs138637932	L>V	A:764	(3.09, 11.58, 38.21)
13:49039233		Y>H	A:771	(0.12, 21.46, 39.69)

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
13:48919281	rs587778870	S>L	A:149	(-22.36, -11.76, 44.60)
13:48953743	rs587778847	G>V	A:449	(-26.25, -14.44, 15.17)
13:48954351	rs587778848	L>P	A:491	(-23.00, -13.27, 19.06)
13:49027133	rs137853292	S>L	A:567	(-3.75, -4.06, 22.89)
13:49030452	rs587778866	K>E	A:643	(-0.42, 8.20, 8.91)
13:49030485	rs483352690	V>M	A:654	(-11.61, 8.31, 26.82)
13:49033836	rs587778834	A>D	A:658	(-13.31, 10.98, 32.10)
13:49033844	rs137853294	R>W	A:661	(-16.78, 8.46, 34.73)
13:49033857	rs483352689	L>R	A:665	(-16.66, 12.68, 41.63)
13:49033964	rs587778859	D>N	A:701	(-12.28, 5.15, 37.17)
13:49037894	rs137853296	C>R	A:712	(-6.01, 17.67, 46.87)
13:49037957	rs587778835	H>Y	A:733	(-22.51, 0.73, 35.67)

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
13:48881439	COSM1367121	E>G	A:54	(-20.61, -9.97, 74.33)
13:48881522	COSM1367136	S>P	A:82	(-16.50, -1.18, 66.27)
13:48919305	COSM4047919	V>A	A:157	(-32.88, -16.32, 40.08)
13:48923137	COSM4853497	W>C	A:195	(-39.30, -24.90, 43.64)
13:48941649	COSM1367192	R>L	A:320	(-32.35, -37.07, 45.70)
13:48941654	COSM1367201	E>K	A:322	(-31.52, -31.98, 52.91)
13:48941658	COSM1367203	E>G	A:323	(-27.93, -34.65, 51.09)
13:48941672	COSM1367206	N>D	A:328	(-23.46, -26.30, 48.39)
13:48947576	COSM1367214	I>T	A:388	(-35.02, -7.72, 14.52)
13:48953748	COSM176711	R>C	A:451	(-31.24, -15.41, 11.79)
13:48954342	COSM254915	A>V	A:488	(-19.16, -10.44, 18.14)
13:48954347	COSM1607123	A>S	A:490	(-24.31, -10.14, 16.88)
13:48954348	COSM1607125	A>V	A:490	(-24.31, -10.14, 16.88)
13:48955428	COSM35888	P>L	A:515	(-16.01, -9.63, 28.28)
13:48955482	COSM1367243	E>G	A:533	(-20.55, 4.09, 15.39)
13:48955551	COSM1367251	R>Q	A:556	(-16.71, -3.01, 30.32)
13:48955571	COSM1367255	W>R	A:563	(-6.12, 1.61, 27.96)
13:49030485	COSM35800	V>L	A:654	(-11.61, 8.31, 26.82)
13:49033833	COSM212940	L>P	A:657	(-16.06, 8.38, 29.95)
13:49033838	COSM327254	Y>H	A:659	(-14.66, 16.52, 32.47)
13:49033839	COSM35346	Y>F	A:659	(-14.66, 16.52, 32.47)
13:49033844	COSM1367287	R>W	A:661	(-16.78, 8.46, 34.73)
13:49033857	COSM5027771	L>R	A:665	(-16.66, 12.68, 41.63)
13:49033926	COSM942	L>P	A:688	(-4.56, 9.24, 29.56)
13:49033955	COSM1367294	R>G	A:698	(-3.33, -0.35, 35.85)
13:49033967	COSM76180	Q>K	A:702	(-7.86, 2.86, 38.98)
13:49037877	COSM883	C>F	A:706	(-5.28, 8.94, 41.92)
13:49037912	COSM1367307	D>N	A:718	(-9.28, 16.97, 54.04)
13:49037913	COSM1367309	D>G	A:718	(-9.28, 16.97, 54.04)
13:49037931	COSM1756817	I>N	A:724	(-12.43, 9.59, 46.81)
13:49037943	COSM40941	Y>C	A:728	(-16.05, 4.87, 41.97)
13:49039183	COSM916	V>G	A:754	(-0.95, 0.82, 47.80)
13:49039189	COSM1140402	Y>C	A:756	(-1.19, 8.20, 45.58)

4ELJ.A | RB1.

4ELJ.A | RB1

General Structure Information

Variant Set Distributions

Ripley’s K Analysis Plots

Variant Set Comparisons

Pathogenic Proximity Analysis

Mapped Variants

[+] ExAC Missense Variants

[+] ClinVar Missense Variants

[+] COSMIC Missense Variants