2V5O.A | IGF2R

General Structure Information

PDB ID	2v5o
HGNC Gene Label(s)	IGF2R
Structure Name	structure of human igf2r domains 11-14
Resolution	2.91Å
Reference	AUTH J.BROWN,C.DELAINE,O.J.ZACCHEO,C.SIEBOLD,R.J.GILBERT,AUTH 2 G.VAN BOXEL,A.DENLEY,J.C.WALLACE,A.B.HASSAN,B.E.FORBES,AUTH 3 E.Y.JONESTITL STRUCTURE AND FUNCTIONAL ANALYSIS OF THE IGF-II/IGF2RTITL 2 INTERACTIONREF EMBO J. V. 27 265 2008REFN ISSN 0261-4189PMID 18046459DOI 10.1038/SJ.EMBOJ.7601938

Variant Set Distributions

ExAC Variants

Number Of Residues	604
Number Of SNVs	160
Number Of Permutations	54034
Optimal Distance Threshold	9.0
K Statistic	0.017
p-value	0.597

COSMIC

Number Of Residues	604
Number Of SNVs	12
Number Of Permutations	13906
Optimal Distance Threshold	36.0
K Statistic	0.53
p-value	0.531

Ripley’s K Analysis Plots

ExACCOSMIC

Variant Set Comparisons

Cosmic vs. ExAC

Number Of ExAC SNVs	160
Number Of COSMIC SNVs	12
Optimal Distance Threshold	56.0
K Statistic	0.139
p-value	0.412

Pathogenic Proximity Analysis

COSMIC PathProx Analysis

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
6:160493050		V>L	A:1518	(51.54, -15.91, 10.62)
6:160493053		T>A	A:1519	(54.51, -16.50, 8.13)
6:160493820		L>V	A:1532	(48.38, -13.94, 23.93)
6:160493839		F>Y	A:1538	(43.15, -10.78, 27.82)
6:160493856		E>Q	A:1544	(32.13, 5.71, 30.28)
6:160493860	rs199789899	K>R	A:1545	(30.46, 1.14, 33.36)
6:160493874	rs137918443	M>V	A:1550	(39.18, -10.71, 24.03)
6:160493880	COSM1662244	I>V	A:1552	(43.89, -14.88, 21.70)
6:160493881		I>T	A:1552	(43.89, -14.88, 21.70)
6:160493885		C>W	A:1553	(43.49, -18.48, 19.42)
6:160493904		P>S	A:1560	(28.94, -17.89, 24.56)
6:160493907		P>S	A:1561	(29.88, -21.89, 23.90)
6:160493913	COSM320937	V>M	A:1563	(32.51, -16.85, 21.29)
6:160494247		A>T	A:1565	(34.13, -11.92, 21.65)
6:160494274		V>M	A:1574	(31.55, -9.60, 18.59)
6:160494304	rs140858283	V>M	A:1584	(48.17, -6.89, 6.77)
6:160494322		L>V	A:1590	(42.63, -12.37, 14.03)
6:160494332		K>R	A:1593	(34.00, -15.96, 11.30)
6:160494344		P>R	A:1597	(22.45, -10.93, 15.18)
6:160494361		G>S	A:1603	(21.93, -12.21, 8.95)
6:160494362	rs201529415	G>D	A:1603	(21.93, -12.21, 8.95)
6:160494391	rs375863720	V>M	A:1613	(50.67, -3.22, 16.16)
6:160494409	rs629849	R>G	A:1619	(54.20, -2.58, 29.13)
6:160494410		R>T	A:1619	(54.20, -2.58, 29.13)
6:160494419		N>S	A:1622	(51.16, -4.05, 25.83)
6:160494421		R>W	A:1623	(45.36, -4.38, 27.57)
6:160494434		I>T	A:1627	(40.40, 1.70, 17.05)
6:160494475	rs200330928	H>Y	A:1641	(50.09, -1.95, 20.06)
6:160494482		P>L	A:1643	(56.47, -7.19, 21.55)
6:160494500	rs142013128	A>V	A:1649	(64.64, -3.33, 14.75)
6:160494792	rs568872578	E>K	A:1651	(65.80, 0.82, 11.63)
6:160494801		V>M	A:1654	(71.63, 7.57, 10.16)
6:160494811	rs532391090	G>E	A:1657	(80.58, 9.24, 9.94)
6:160494813		S>R	A:1658	(82.02, 9.03, 13.39)
6:160494817		S>F	A:1659	(78.58, 10.02, 14.76)
6:160494846	COSM741316	R>C	A:1669	(57.33, 5.64, 22.93)
6:160494847	COSM1075609	R>H	A:1669	(57.33, 5.64, 22.93)
6:160494856		G>V	A:1672	(50.45, 11.61, 18.22)
6:160494862		E>G	A:1674	(48.19, 16.84, 16.63)
6:160494871		D>G	A:1677	(44.43, 23.94, 10.59)
6:160494901	rs144685922	N>S	A:1687	(40.00, 20.45, 14.52)
6:160494915	rs562847817	I>V	A:1692	(52.91, 11.95, 12.54)
6:160494921		I>V	A:1694	(59.03, 8.47, 13.23)
6:160494928	rs11552587	Q>R	A:1696	(57.52, 2.87, 16.86)
6:160494930		P>S	A:1697	(53.75, 2.34, 14.49)
6:160494940		P>H	A:1700	(46.43, 3.69, 20.23)
6:160494942	rs548541444	M>V	A:1701	(44.44, 7.66, 18.58)
6:160494964	rs199662672	A>V	A:1708	(46.41, -0.49, 11.80)
6:160494969	rs185442936	A>T	A:1710	(49.82, 3.52, 10.63)
6:160494979		C>Y	A:1713	(46.91, 9.68, 9.50)
6:160494984		V>L	A:1715	(41.40, 13.03, 9.69)
6:160496889		R>Q	A:1726	(52.11, 1.74, 6.55)
6:160496898		G>E	A:1729	(62.81, 2.89, 6.49)
6:160496913		N>S	A:1734	(72.40, 15.05, 2.61)
6:160496946		E>G	A:1745	(54.80, 2.31, 2.60)
6:160496967	rs142965315	A>V	A:1752	(45.92, 9.24, -10.06)
6:160496982		N>S	A:1757	(49.93, 3.28, -3.72)
6:160496991		S>L	A:1760	(54.89, 10.23, 3.18)
6:160496996		I>V	A:1762	(59.23, 13.58, 7.48)
6:160497000	COSM207405	A>V	A:1763	(61.93, 16.81, 6.56)
6:160497006		H>R	A:1765	(65.09, 21.27, 8.23)
6:160497014		R>G	A:1768	(70.93, 24.07, 17.97)
6:160497020		V>M	A:1770	(63.51, 24.11, 24.53)
6:160497023		S>G	A:1771	(61.43, 22.73, 21.10)
6:160499237		T>M	A:1774	(55.73, 19.54, 15.74)
6:160499258	rs148892832	S>N	A:1781	(52.15, 17.06, -4.73)
6:160499260	rs142698228	E>K	A:1782	(47.81, 16.34, -4.54)
6:160499272		V>M	A:1786	(55.72, 16.85, 2.06)
6:160499278		E>Q	A:1788	(59.26, 21.00, 7.60)
6:160499296	rs371430710 COSM240201	V>I	A:1794	(69.14, 16.77, 13.35)
6:160499308		E>Q	A:1798	(78.41, 22.69, 18.51)
6:160499309		E>G	A:1798	(78.41, 22.69, 18.51)
6:160499319		M>I	A:1801	(83.88, 28.38, 21.42)
6:160499321		D>V	A:1802	(84.77, 28.77, 25.65)
6:160499330		T>S	A:1805	(84.70, 28.94, 30.31)
6:160499350	rs189986553	L>F	A:1812	(86.09, 41.50, 28.49)
6:160499351		L>P	A:1812	(86.09, 41.50, 28.49)
6:160499354	rs150924677	Y>C	A:1813	(85.19, 39.58, 34.15)
6:160499362		N>D	A:1816	(87.26, 28.34, 35.39)
6:160499369		S>F	A:1818	(86.61, 23.56, 35.61)
6:160499373	rs368727465	S>R	A:1819	(86.80, 23.53, 39.62)
6:160499374		L>F	A:1820	(82.90, 22.85, 39.73)
6:160499380		T>S	A:1822	(85.97, 17.36, 39.64)
6:160499381	rs115412888	T>M	A:1822	(85.97, 17.36, 39.64)
6:160500621		D>N	A:1830	(60.82, 16.04, 49.12)
6:160500625	rs200083721	S>L	A:1831	(62.70, 11.70, 47.99)
6:160500627		R>C	A:1832	(62.23, 14.92, 44.93)
6:160500628	rs8191904	R>H	A:1832	(62.23, 14.92, 44.93)
6:160500639	rs140658120	V>I	A:1836	(74.43, 17.39, 39.24)
6:160500661	rs545752120	V>A	A:1843	(75.70, 9.31, 35.68)
6:160500686		K>N	A:1851	(72.39, 8.01, 27.00)
6:160500712	rs8191905	G>D	A:1860	(67.20, 3.58, 40.53)
6:160500718		K>R	A:1862	(64.68, 3.51, 35.73)
6:160500723	rs201170949	A>T	A:1864	(65.49, 11.13, 34.35)
6:160500724		A>V	A:1864	(65.49, 11.13, 34.35)
6:160500735		R>W	A:1868	(71.83, 16.16, 25.25)
6:160500736		R>Q	A:1868	(71.83, 16.16, 25.25)
6:160500764		R>S	A:1877	(71.12, 36.35, 36.07)
6:160500778		A>V	A:1882	(74.83, 35.48, 37.78)
6:160500783	rs372315069 COSM1075615	V>I	A:1884	(72.85, 30.54, 33.92)
6:160500789	rs562128670	S>G	A:1886	(71.57, 25.40, 30.49)
6:160500804		D>N	A:1891	(63.68, 12.36, 29.17)
6:160500808	rs149633151	R>H	A:1892	(58.65, 12.71, 26.05)
6:160500816	rs370980819	P>A	A:1895	(51.77, 13.07, 32.46)
6:160501166		D>N	A:1898	(42.13, 16.04, 31.09)
6:160501172	rs373759284	G>S	A:1900	(45.60, 19.58, 35.71)
6:160501175	rs76130099	V>I	A:1901	(45.84, 17.13, 38.51)
6:160501179		P>L	A:1902	(49.46, 16.38, 38.98)
6:160501196	rs140022962	I>V	A:1908	(49.35, 1.18, 44.08)
6:160501197		I>T	A:1908	(49.35, 1.18, 44.08)
6:160501198	rs8191908	I>M	A:1908	(49.35, 1.18, 44.08)
6:160501203		N>S	A:1910	(44.43, -3.94, 41.07)
6:160501213		S>R	A:1913	(53.47, -0.51, 40.60)
6:160501217		E>K	A:1915	(56.32, 4.03, 36.95)
6:160501230		I>T	A:1919	(44.84, 0.89, 29.08)
6:160501242	rs368781979 COSM3928206	A>V	A:1923	(39.05, 3.72, 27.18)
6:160501259		T>A	A:1929	(46.28, 11.88, 41.52)
6:160501266	rs150759811	A>V	A:1931	(50.39, 6.75, 45.49)
6:160501268	rs372344925	D>N	A:1932	(47.28, 4.04, 46.86)
6:160501286	rs532240139	E>K	A:1938	(41.72, 10.89, 43.63)
6:160501287		E>G	A:1938	(41.72, 10.89, 43.63)
6:160501305		H>P	A:1944	(50.31, 12.69, 27.39)
6:160501307		S>A	A:1945	(53.70, 16.59, 27.37)
6:160504984		N>D	A:1946	(54.45, 18.16, 24.02)
6:160504990		Y>H	A:1948	(61.03, 16.34, 24.96)
6:160504991		Y>C	A:1948	(61.03, 16.34, 24.96)
6:160504994	rs373029226 COSM1441968 COSM1075619	R>Q	A:1949	(62.27, 15.86, 31.87)
6:160505013		F>L	A:1955	(76.55, 28.73, 39.18)
6:160505022		D>E	A:1958	(80.32, 32.69, 48.57)
6:160505026		D>Y	A:1960	(83.58, 31.33, 52.23)
6:160505049	rs529803102	Q>H	A:1967	(70.94, 22.62, 47.36)
6:160505050	rs538340074	V>I	A:1968	(66.85, 22.23, 45.11)
6:160505065		R>C	A:1973	(54.61, 21.60, 35.76)
6:160505066	rs375077970	R>H	A:1973	(54.61, 21.60, 35.76)
6:160505075	rs145118454	D>V	A:1976	(62.65, 22.51, 35.41)
6:160505083		F>L	A:1979	(69.79, 22.72, 40.78)
6:160505107		C>R	A:1987	(83.31, 36.26, 42.27)
6:160505122		L>M	A:1992	(90.89, 44.92, 36.92)
6:160505137	rs370080412	V>I	A:1997	(93.44, 49.32, 23.16)
6:160505141		Q>R	A:1998	(90.35, 53.15, 21.66)
6:160505158		D>N	A:2004	(99.42, 52.37, 31.89)
6:160505164		R>W	A:2006	(100.09, 50.00, 35.71)
6:160505185		G>R	A:2013	(94.26, 52.95, 49.67)
6:160505195		S>F	A:2016	(90.66, 62.17, 48.75)
6:160505207	rs1805075	N>S	A:2020	(80.63, 71.13, 49.04)
6:160505208		N>K	A:2020	(80.63, 71.13, 49.04)
6:160506032		Y>C	A:2025	(86.71, 58.54, 50.27)
6:160506034		I>V	A:2026	(88.59, 57.88, 43.88)
6:160506055		Y>H	A:2033	(92.80, 48.94, 49.23)
6:160506074		C>Y	A:2039	(82.98, 51.27, 52.02)
6:160506076	rs201916817	S>P	A:2040	(82.00, 47.99, 50.38)
6:160506086		A>V	A:2043	(84.43, 49.67, 46.39)
6:160506106		T>A	A:2050	(78.95, 66.00, 56.58)
6:160506109	rs535817203	T>A	A:2051	(77.27, 63.51, 59.82)
6:160506123		Q>H	A:2055	(76.62, 56.98, 49.54)
6:160506136		V>I	A:2060	(86.12, 47.29, 40.89)
6:160506143		T>M	A:2062	(81.68, 47.48, 36.71)
6:160509071	rs201217610	K>R	A:2071	(88.58, 63.55, 27.47)
6:160509073		V>I	A:2072	(90.79, 58.75, 29.19)
6:160509083		T>M	A:2075	(82.87, 53.73, 33.91)
6:160509091		K>E	A:2078	(76.11, 47.66, 39.94)
6:160509101	rs151080511	P>L	A:2081	(70.01, 52.50, 46.18)
6:160509104		C>F	A:2082	(68.71, 55.89, 42.83)
6:160509113		N>I	A:2085	(65.50, 50.18, 38.60)
6:160509122		A>G	A:2088	(74.93, 54.47, 41.42)
6:160509130		V>M	A:2091	(81.94, 58.89, 34.91)
6:160509136		E>Q	A:2093	(86.26, 63.15, 32.58)
6:160509148	rs370183140	T>A	A:2097	(98.75, 66.59, 32.23)
6:160509155		T>M	A:2099	(100.82, 66.23, 36.66)
6:160509157		V>M	A:2100	(100.31, 62.72, 39.04)
6:160509166		P>A	A:2103	(90.83, 63.80, 41.94)
6:160510144		D>G	A:2109	(73.01, 63.48, 35.85)
6:160510149		D>H	A:2111	(67.85, 61.32, 34.71)
6:160510150	rs371845257	D>G	A:2111	(67.85, 61.32, 34.71)
6:160510164		Y>H	A:2116	(79.89, 62.81, 35.10)
6:160510177	rs376138460	D>A	A:2120	(94.16, 66.81, 34.84)
6:160510197	rs142990243	V>M	A:2127	(104.15, 56.87, 25.44)

2V5O.A | IGF2R.

2V5O.A | IGF2R

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