4B3F.X | IGHMBP2

General Structure Information

PDB ID	4b3f
HGNC Gene Label(s)	IGHMBP2
Structure Name	crystal structure of 1ghmbp2 helicase
Resolution	2.5Å
Reference	AUTH S.C.LIM,M.W.BOWLER,T.F.LAI,H.SONGTITL THE IGHMBP2 HELICASE STRUCTURE REVEALS THE MOLECULAR BASISTITL 2 FOR DISEASE-CAUSING MUTATIONS IN DMSA1.REF NUCLEIC ACIDS RES. V. 40 11009 2012REFN ISSN 0305-1048PMID 22965130DOI 10.1093/NAR/GKS792

Variant Set Distributions

ExAC Variants

Number Of Residues	625
Number Of SNVs	185
Number Of Permutations	75226
Optimal Distance Threshold	6.0
K Statistic	0.008
p-value	0.822

ClinVar

Number Of Residues	625
Number Of SNVs	8
Number Of Permutations	4982
Optimal Distance Threshold	16.0
K Statistic	0.214
p-value	0.234

COSMIC

Number Of Residues	625
Number Of SNVs	5
Number Of Permutations	456
Optimal Distance Threshold	28.0
K Statistic	0.2
p-value	0.796

Ripley’s K Analysis Plots

ExACClinVarCOSMIC

Variant Set Comparisons

ClinVar vs. ExAC

Number Of ExAC SNVs	185
Number Of ClinVar SNVs	8
Optimal Distance Threshold	11.0
K Statistic	0.068
p-value	0.241

Cosmic vs. ExAC

Number Of ExAC SNVs	185
Number Of COSMIC SNVs	5
Optimal Distance Threshold	19.0
K Statistic	-0.155
p-value	0.52

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
11:68671428		S>L	X:3	(33.20, 33.32, -4.24)
11:68671461		L>P	X:14	(27.18, 47.02, 1.62)
11:68671469		L>V	X:17	(25.86, 49.01, 6.29)
11:68671488		A>V	X:23	(19.29, 55.57, 10.17)
11:68673553	rs199586231	I>V	X:35	(16.53, 68.61, 20.58)
11:68673583		V>M	X:45	(25.46, 64.27, 22.74)
11:68673593	rs144361739	L>Q	X:48	(28.11, 73.46, 25.64)
11:68673597		K>N	X:49	(29.33, 76.92, 26.05)
11:68673615	rs201692151	Q>H	X:55	(46.50, 74.78, 19.28)
11:68673616	rs201649839	R>C	X:56	(50.43, 72.23, 20.55)
11:68673617	rs571887680 COSM2043086	R>H	X:56	(50.43, 72.23, 20.55)
11:68673619		T>P	X:57	(51.01, 69.46, 15.71)
11:68673634		R>G	X:62	(45.82, 63.83, 13.50)
11:68673635		R>Q	X:62	(45.82, 63.83, 13.50)
11:68673658	rs563922049 COSM1605142	R>G	X:70	(34.72, 80.58, 29.45)
11:68673662		R>L	X:71	(37.99, 81.03, 34.98)
11:68673665		Y>C	X:72	(33.05, 77.42, 35.91)
11:68673692		N>S	X:81	(30.07, 62.72, 28.58)
11:68673701	rs549801214	T>I	X:84	(34.59, 57.76, 23.26)
11:68673704		S>F	X:85	(38.03, 57.54, 22.31)
11:68675640	rs372940951	A>V	X:95	(29.84, 83.92, 17.75)
11:68675642		N>D	X:96	(30.15, 81.64, 14.27)
11:68675660	rs35610053	A>S	X:102	(34.89, 71.26, 11.89)
11:68675676		T>N	X:107	(42.28, 61.48, 21.35)
11:68675678		R>W	X:108	(42.95, 62.35, 26.92)
11:68675679		R>Q	X:108	(42.95, 62.35, 26.92)
11:68675681	rs141451851	V>L	X:109	(37.77, 61.86, 27.15)
11:68675684		T>A	X:110	(39.14, 63.88, 30.73)
11:68675700	rs181657861	T>M	X:115	(41.44, 65.76, 22.84)
11:68675702	rs554952116	V>M	X:116	(39.94, 66.90, 18.91)
11:68675710	rs534344339	F>L	X:118	(40.95, 68.70, 14.07)
11:68675737		S>R	X:127	(41.34, 79.75, 13.60)
11:68675741		D>N	X:129	(40.98, 82.34, 19.82)
11:68675749		E>D	X:131	(39.44, 84.36, 23.25)
11:68675763	rs199841148	L>Q	X:136	(32.01, 69.62, 20.81)
11:68675775		A>G	X:140	(28.18, 60.15, 12.57)
11:68675778		N>S	X:141	(31.81, 57.21, 12.73)
11:68675782		D>E	X:142	(31.33, 58.45, 7.84)
11:68675790		Y>C	X:145	(29.14, 53.72, 8.78)
11:68675796	rs138448914	R>Q	X:147	(37.81, 52.01, 8.80)
11:68676003	rs536962342 COSM4036177 COSM401240	A>T	X:151	(36.47, 44.95, 4.61)
11:68676004		A>G	X:151	(36.47, 44.95, 4.61)
11:68676031		S>Y	X:160	(45.58, 33.18, -2.52)
11:68676034		G>V	X:161	(45.91, 33.14, 1.31)
11:68676037		P>L	X:162	(47.02, 33.37, 4.50)
11:68676052		I>T	X:167	(37.32, 32.35, 4.53)
11:68676091		S>N	X:180	(46.77, 19.96, 16.51)
11:68676099	rs548256623	H>Y	X:183	(53.42, 19.98, 23.85)
11:68678911		P>L	X:184	(52.11, 19.57, 27.24)
11:68678924		F>L	X:188	(52.01, 31.92, 31.82)
11:68678926		N>S	X:189	(47.08, 31.91, 35.84)
11:68678956		A>V	X:199	(39.90, 26.35, 26.80)
11:68678962	rs560096	L>S	X:201	(44.56, 22.98, 26.24)
11:68678963		L>F	X:201	(44.56, 22.98, 26.24)
11:68678966		F>L	X:202	(39.93, 23.47, 21.89)
11:68678967	COSM2043114	A>T	X:203	(42.60, 27.08, 21.52)
11:68678968	rs373012350	A>V	X:203	(42.60, 27.08, 21.52)
11:68678970		L>V	X:204	(46.56, 26.73, 21.76)
11:68678982	rs374952782	E>K	X:208	(41.06, 27.06, 10.92)
11:68679004	COSM4036179	P>R	X:215	(29.46, 32.50, 31.00)
11:68679010		G>D	X:217	(31.78, 35.09, 35.90)
11:68679025		T>M	X:222	(41.54, 35.29, 32.77)
11:68679039		I>V	X:227	(45.01, 31.81, 25.13)
11:68682304		A>V	X:242	(37.69, 44.51, 20.25)
11:68682306		P>S	X:243	(34.36, 45.73, 19.81)
11:68682309		S>A	X:244	(35.38, 48.00, 22.84)
11:68682315	rs377678376	I>V	X:246	(36.37, 49.45, 27.74)
11:68682318	COSM1210376	A>T	X:247	(37.86, 45.72, 25.90)
11:68682321	rs201112136	V>M	X:248	(41.13, 46.95, 24.13)
11:68682346	rs148095551	A>G	X:256	(50.96, 44.68, 31.41)
11:68682349		L>P	X:257	(50.00, 43.47, 35.01)
11:68682360	rs141836800	R>W	X:261	(57.77, 42.34, 24.32)
11:68682369	rs139497493	R>C	X:264	(45.78, 50.53, 22.24)
11:68682387	rs201054207	R>C	X:270	(40.49, 52.14, 31.56)
11:68682394		L>P	X:272	(45.13, 53.12, 34.36)
11:68682402	rs10896380	I>V	X:275	(46.33, 51.46, 29.92)
11:68682411	rs144681826	H>D	X:278	(51.53, 50.04, 26.97)
11:68682424		A>V	X:282	(53.82, 56.55, 24.20)
11:68682433	rs201188656	A>V	X:285	(57.66, 59.22, 22.84)
11:68682435	COSM194731	R>W	X:286	(58.48, 55.00, 25.37)
11:68682436	rs200566598	R>Q	X:286	(58.48, 55.00, 25.37)
11:68682441		D>N	X:288	(65.11, 56.40, 19.68)
11:68682447	rs370988994	A>T	X:290	(63.12, 64.08, 19.75)
11:68682452		Q>H	X:291	(64.34, 64.17, 16.51)
11:68682453		I>L	X:292	(59.00, 63.51, 15.76)
11:68682454		I>T	X:292	(59.00, 63.51, 15.76)
11:68682456		V>I	X:293	(58.67, 67.00, 18.48)
11:68682459		A>T	X:294	(61.11, 68.92, 15.90)
11:68682460	rs531698017	A>G	X:294	(61.11, 68.92, 15.90)
11:68682463		D>G	X:295	(59.37, 67.71, 12.78)
11:68682466	rs375554721	I>N	X:296	(55.44, 68.61, 15.52)
11:68682472		K>R	X:298	(59.77, 73.48, 13.72)
11:68682473	rs536156719	K>N	X:298	(59.77, 73.48, 13.72)
11:68682474		D>N	X:299	(54.65, 72.46, 11.81)
11:68682477		I>V	X:300	(52.69, 74.13, 15.60)
11:68682480	rs139635469	D>N	X:301	(56.92, 77.07, 15.40)
11:68682484		Q>R	X:302	(54.86, 78.06, 10.30)
11:68685210		N>H	X:307	(48.77, 84.83, 11.89)
11:68685216	rs200079527	K>E	X:309	(47.69, 88.28, 6.11)
11:68685243		N>D	X:318	(54.95, 80.69, 0.61)
11:68685250	COSM257150	R>Q	X:320	(49.68, 76.52, 1.15)
11:68685289		R>T	X:333	(62.21, 60.31, 9.96)
11:68685297	rs145076368	A>T	X:336	(59.59, 54.19, 10.82)
11:68685306	rs149045005	L>F	X:339	(57.35, 49.24, 10.99)
11:68685309		E>K	X:340	(60.54, 49.11, 15.30)
11:68685314	rs547681612	S>R	X:341	(57.04, 49.79, 17.42)
11:68685322	rs368481743	S>L	X:344	(58.80, 44.87, 18.56)
11:68685327	rs567322475	N>D	X:346	(55.03, 39.81, 20.82)
11:68685339	rs371984479	A>P	X:350	(42.82, 46.97, 18.46)
11:68696654	rs142062146	A>V	X:355	(42.65, 47.18, 12.56)
11:68696656		S>P	X:356	(42.29, 49.17, 9.34)
11:68696672	rs201060167 COSM1193689 CM034530	L>P	X:361	(48.42, 47.44, 10.65)
11:68696686	COSM690266	E>K	X:366	(50.28, 39.80, 3.98)
11:68696690		S>I	X:367	(51.96, 37.22, 6.40)
11:68696696		F>Y	X:369	(49.87, 39.63, 12.81)
11:68696698	rs200007067	D>N	X:370	(50.29, 34.07, 13.36)
11:68696701		V>M	X:371	(46.65, 34.56, 15.92)
11:68696720		C>Y	X:377	(32.54, 38.71, 19.14)
11:68696734		E>Q	X:382	(30.28, 39.27, 10.74)
11:68696737		A>T	X:383	(31.67, 43.64, 9.51)
11:68696744	rs372477029	C>S	X:385	(35.21, 40.95, 12.60)
11:68696746		W>R	X:386	(35.57, 38.91, 8.02)
11:68696767		R>G	X:393	(47.46, 31.41, 10.00)
11:68696783	rs35193202	A>V	X:398	(35.47, 35.66, 22.71)
11:68696788		D>N	X:400	(28.07, 35.55, 26.02)
11:68696791		H>Y	X:401	(26.23, 33.52, 22.18)
11:68696804		P>R	X:405	(23.47, 42.05, 20.79)
11:68696823	rs199753365	H>Q	X:411	(14.36, 46.61, 14.34)
11:68700805		R>H	X:425	(27.47, 32.71, 11.89)
11:68700822		G>S	X:431	(29.58, 24.05, 18.52)
11:68700826	rs370414354	A>V	X:432	(31.67, 21.44, 20.15)
11:68700837	rs138327042	R>W	X:436	(35.28, 23.86, 24.07)
11:68700838	COSM366083	R>Q	X:436	(35.28, 23.86, 24.07)
11:68700847	rs373649545	T>M	X:439	(31.44, 26.14, 33.99)
11:68700858		R>C	X:443	(29.39, 37.92, 39.09)
11:68700859		R>H	X:443	(29.39, 37.92, 39.09)
11:68700868		Q>P	X:446	(23.56, 29.10, 45.03)
11:68700869	rs149628807	Q>H	X:446	(23.56, 29.10, 45.03)
11:68700871	rs144240271	A>G	X:447	(20.13, 31.43, 43.42)
11:68700873	rs139000973	I>V	X:448	(21.33, 34.71, 41.32)
11:68700879	rs374363750	R>C	X:450	(20.72, 27.37, 40.92)
11:68700880		R>H	X:450	(20.72, 27.37, 40.92)
11:68700884		W>C	X:451	(17.37, 32.94, 35.50)
11:68700892		D>G	X:454	(18.92, 26.33, 34.22)
11:68700894		T>P	X:455	(17.29, 29.87, 31.34)
11:68700895		T>S	X:455	(17.29, 29.87, 31.34)
11:68700898		M>R	X:456	(20.36, 31.23, 28.73)
11:68700904		L>R	X:458	(22.35, 24.11, 28.98)
11:68700930		V>L	X:467	(30.24, 33.47, 45.42)
11:68701266	rs61731907	D>E	X:474	(27.88, 38.42, 54.85)
11:68701267		L>F	X:475	(28.74, 43.09, 53.49)
11:68701274		G>A	X:477	(28.06, 47.02, 58.31)
11:68701322		T>I	X:493	(2.65, 45.78, 40.46)
11:68701325	rs377680312	A>V	X:494	(0.06, 42.79, 40.44)
11:68701327	rs201964221	G>S	X:495	(-2.88, 44.87, 41.06)
11:68701328		G>A	X:495	(-2.88, 44.87, 41.06)
11:68701376		N>S	X:511	(6.15, 52.94, 36.15)
11:68701378		P>S	X:512	(5.70, 56.29, 38.22)
11:68701934	rs137852665	E>K	X:514	(7.98, 50.44, 38.93)
11:68701940		R>C	X:516	(6.15, 55.47, 44.66)
11:68701941	rs373017768	R>H	X:516	(6.15, 55.47, 44.66)
11:68701946	rs373828321 COSM194733	V>I	X:518	(13.12, 51.39, 43.60)
11:68701950		S>N	X:519	(13.10, 54.40, 46.32)
11:68701954	rs375645505	L>F	X:520	(10.75, 52.56, 49.49)
11:68701955		H>Y	X:521	(14.69, 47.83, 48.30)
11:68701965		A>G	X:524	(16.28, 49.59, 52.98)
11:68701971		V>A	X:526	(21.07, 52.62, 52.65)
11:68701982	rs372447032	V>I	X:530	(24.23, 48.79, 51.90)
11:68701985		P>T	X:531	(27.09, 50.80, 50.52)
11:68701991	rs374185933 COSM378978	R>C	X:533	(30.11, 52.37, 47.61)
11:68701992	rs369816416	R>H	X:533	(30.11, 52.37, 47.61)
11:68701997	rs140221316	I>V	X:535	(23.52, 49.63, 45.16)
11:68702001		A>V	X:536	(22.41, 49.07, 41.09)
11:68702004		V>E	X:537	(19.27, 51.11, 39.83)
11:68702021		L>V	X:543	(11.78, 57.43, 30.55)
11:68702783		Q>R	X:550	(14.06, 62.90, 38.00)
11:68702786		S>I	X:551	(13.73, 60.62, 42.44)
11:68702821		S>P	X:563	(20.60, 51.02, 31.09)
11:68702827		D>N	X:565	(22.24, 48.38, 27.06)
11:68702843		R>Q	X:570	(29.62, 47.32, 35.67)
11:68702857		V>L	X:575	(20.96, 44.76, 41.40)
11:68702872	rs137852667	V>I	X:580	(8.45, 49.60, 33.10)
11:68702888	rs146450269	K>R	X:585	(-2.32, 46.53, 26.17)
11:68703711		V>A	X:588	(5.83, 43.08, 26.78)
11:68703714		G>V	X:589	(8.57, 45.33, 24.58)
11:68703729		D>A	X:594	(15.21, 36.89, 26.81)
11:68703731		R>W	X:595	(20.26, 38.01, 24.23)
11:68703732	rs143766075	R>Q	X:595	(20.26, 38.01, 24.23)
11:68703743	rs199770424	V>M	X:599	(22.55, 41.12, 31.16)
11:68703753		T>S	X:602	(23.89, 38.58, 35.56)
11:68703756	rs151079750	R>H	X:603	(25.52, 42.24, 35.82)
11:68703762	rs141107419	R>Q	X:605	(28.80, 39.72, 43.85)
11:68703764	rs536556753	R>S	X:606	(26.63, 39.58, 48.34)
11:68703770	rs573382473	V>M	X:608	(18.34, 40.39, 42.74)
11:68703774		A>V	X:609	(15.51, 43.20, 42.96)
11:68703779		I>V	X:611	(10.18, 46.12, 40.77)
11:68703792	rs201640213	R>H	X:615	(-2.06, 40.82, 36.25)
11:68703797		V>I	X:617	(5.69, 40.04, 32.79)
11:68703801		N>S	X:618	(3.49, 36.44, 33.39)
11:68703802	rs577924460	N>K	X:618	(3.49, 36.44, 33.39)
11:68703821		T>A	X:625	(10.17, 31.51, 33.89)
11:68703857	rs201563456 CM041023	R>C	X:637	(8.14, 41.84, 49.72)
11:68703858	rs564004016	R>H	X:637	(8.14, 41.84, 49.72)
11:68703861		T>M	X:638	(2.63, 43.19, 47.36)
11:68703864	rs11600808	A>V	X:639	(2.82, 46.94, 46.60)
11:68703887	rs77822399	V>I	X:647	(-6.72, 52.12, 44.77)

4B3F.X | IGHMBP2.

4B3F.X | IGHMBP2

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

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
11:68678964	rs724159958	F>V	X:202	(39.93, 23.47, 21.89)
11:68678998	rs137852666	H>R	X:213	(30.50, 30.69, 25.95)
11:68696697	rs137852670	F>L	X:369	(49.87, 39.63, 12.81)
11:68696708	rs724159959	V>G	X:373	(42.12, 37.52, 19.36)
11:68701934	rs137852665	E>K	X:514	(7.98, 50.44, 38.93)
11:68701976	rs724159960	A>T	X:528	(21.21, 48.54, 56.75)
11:68701985	rs756985703	P>T	X:531	(27.09, 50.80, 50.52)
11:68702872	rs137852667	V>I	X:580	(8.45, 49.60, 33.10)

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
11:68673617	COSM2043086	R>H	X:56	(50.43, 72.23, 20.55)
11:68673658	COSM1605142	R>W	X:70	(34.72, 80.58, 29.45)
11:68682435	COSM194731	R>W	X:286	(58.48, 55.00, 25.37)
11:68701342	COSM3703654	E>Q	X:500	(2.82, 51.77, 31.19)
11:68701991	COSM378978	R>C	X:533	(30.11, 52.37, 47.61)