3BIC.B | MUT – ASTRID

3BIC.B | MUT

General Structure Information

PDB ID	3bic
HGNC Gene Label(s)	MUT
Structure Name	crystal structure of human methylmalonyl-coa mutase
Resolution	2.6Å
Reference	AUTH D.S.FROESE,G.KOCHAN,J.R.MUNIZ,X.WU,C.GILEADI,E.UGOCHUKWU,AUTH 2 E.KRYSZTOFINSKA,R.A.GRAVEL,U.OPPERMANN,W.W.YUETITL STRUCTURES OF THE HUMAN GTPASE MMAA AND VITAMINTITL 2 B12-DEPENDENT METHYLMALONYL-COA MUTASE AND INSIGHT INTOTITL 3 THEIR COMPLEX FORMATION.REF J.BIOL.CHEM. V. 285 38204 2010REFN ISSN 0021-9258PMID 20876572DOI 10.1074/JBC.M110.177717

Variant Set Distributions

ExAC Variants

Number Of Residues	708
Number Of SNVs	197
Number Of Permutations	82258
Optimal Distance Threshold	17.0
K Statistic	0.1
p-value	0.048

ClinVar

Number Of Residues	708
Number Of SNVs	21
Number Of Permutations	16122
Optimal Distance Threshold	25.0
K Statistic	0.49
p-value	0.002

COSMIC

Number Of Residues	708
Number Of SNVs	9
Number Of Permutations	2455
Optimal Distance Threshold	7.0
K Statistic	0.028
p-value	0.998

Ripley’s K Analysis Plots

ExACClinVarCOSMIC

Variant Set Comparisons

ClinVar vs. ExAC

Number Of ExAC SNVs	197
Number Of ClinVar SNVs	20
Optimal Distance Threshold	25.0
K Statistic	0.225
p-value	0.002

Cosmic vs. ExAC

Number Of ExAC SNVs	197
Number Of COSMIC SNVs	9
Optimal Distance Threshold	7.0
K Statistic	0.018
p-value	0.798

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
6:49427030	rs368296765	Q>H	B:50	(-25.92, 19.22, -4.44)
6:49427019	rs559152765	K>R	B:54	(-28.65, 26.00, 0.37)
6:49427007		D>A	B:58	(-35.11, 27.71, -0.67)
6:49427004		L>R	B:59	(-35.98, 23.64, -3.36)
6:49427001		I>T	B:60	(-40.68, 24.17, -0.99)
6:49426989	rs575038087 COSM396781	P>L	B:64	(-50.37, 29.35, -7.60)
6:49426984		G>R	B:66	(-51.40, 27.29, -2.05)
6:49426980		I>S	B:67	(-50.75, 23.66, -2.61)
6:49426973		I>M	B:69	(-45.24, 20.90, -4.06)
6:49426975	rs115923556	I>V	B:69	(-45.24, 20.90, -4.06)
6:49426965		L>S	B:72	(-38.36, 14.55, -1.94)
6:49426960		S>A	B:74	(-40.75, 9.40, 0.85)
6:49426954		R>G	B:76	(-40.72, 8.98, 6.02)
6:49426945		M>V	B:79	(-46.55, 4.66, 6.19)
6:49426935		P>R	B:82	(-55.58, 4.09, 1.85)
6:49426927		L>F	B:85	(-58.94, -0.34, -5.84)
6:49426923		P>L	B:86	(-59.81, 1.24, -9.56)
6:49426924		P>S	B:86	(-59.81, 1.24, -9.56)
6:49426918		V>M	B:88	(-63.62, 1.00, -5.25)
6:49426902	rs121918251	R>H	B:93	(-56.43, 4.16, -8.38)
6:49426903		R>C	B:93	(-56.43, 4.16, -8.38)
6:49426899	rs535411418 CM050668 CM973221	G>V	B:94	(-61.50, 5.53, -10.74)
6:49426900		G>R	B:94	(-61.50, 5.53, -10.74)
6:49426896	rs190834116	P>L	B:95	(-64.56, 5.62, -12.39)
6:49426870	rs537995137	P>S	B:104	(-59.89, 3.47, -24.83)
6:49426857	COSM1187051 CM012405	R>H	B:108	(-64.21, 14.40, -28.41)
6:49426858	rs121918257	R>C	B:108	(-64.21, 14.40, -28.41)
6:49426821		N>S	B:120	(-76.75, 18.03, -42.65)
6:49426814	rs368780480	F>L	B:122	(-69.46, 16.65, -40.43)
6:49426810		K>E	B:124	(-75.45, 12.95, -43.72)
6:49425765		Q>L	B:131	(-71.07, 6.88, -36.52)
6:49425762		Q>R	B:132	(-73.69, 6.19, -33.28)
6:49425726		R>H	B:144	(-77.80, 36.62, -24.47)
6:49425720	rs528689712	Y>C	B:146	(-80.98, 38.22, -28.62)
6:49425702		R>Q	B:152	(-78.33, 44.92, -28.80)
6:49425696	rs142068898	R>H	B:154	(-75.33, 41.85, -36.60)
6:49425693		G>D	B:155	(-72.15, 40.33, -35.76)
6:49425690		D>V	B:156	(-72.93, 38.30, -33.07)
6:49425666	rs201477610	I>N	B:164	(-81.26, 28.32, -34.18)
6:49425658		V>M	B:167	(-88.30, 24.41, -35.54)
6:49425625	COSM596766	P>S	B:178	(-81.28, 9.25, -37.36)
6:49425611		M>I	B:182	(-77.88, 9.91, -33.59)
6:49425601	rs148331800	M>V	B:186	(-77.09, 20.25, -27.33)
6:49425585		A>E	B:191	(-81.35, 29.45, -24.62)
6:49425577		P>A	B:194	(-85.66, 27.82, -26.68)
6:49425559		I>V	B:200	(-88.32, 18.05, -28.30)
6:49425552	rs576792926	T>I	B:202	(-87.21, 18.28, -34.71)
6:49425550		G>R	B:203	(-88.33, 14.77, -33.50)
6:49425537	rs144034003	G>V	B:207	(-91.30, 10.26, -35.71)
6:49425538		G>R	B:207	(-91.30, 10.26, -35.71)
6:49425532		P>S	B:209	(-90.48, 8.75, -30.09)
6:49425524		E>D	B:211	(-88.49, 8.45, -25.26)
6:49425525	rs558215803	E>G	B:211	(-88.49, 8.45, -25.26)
6:49425513		G>D	B:215	(-78.15, 13.21, -24.94)
6:49425502	rs121918256	N>Y	B:219	(-78.51, 23.37, -18.47)
6:49425479		M>I	B:226	(-69.10, 32.37, -12.19)
6:49425481		M>V	B:226	(-69.10, 32.37, -12.19)
6:49425436	rs145586906	I>V	B:241	(-85.52, 27.32, -16.32)
6:49425422		I>M	B:245	(-85.30, 21.14, -17.88)
6:49425424		I>V	B:245	(-85.30, 21.14, -17.88)
6:49425419	COSM3874628	F>L	B:246	(-83.73, 18.62, -14.06)
6:49425414		Y>C	B:248	(-90.37, 17.53, -20.34)
6:49425411		T>I	B:249	(-86.26, 15.32, -18.99)
6:49423929	rs201459583	I>V	B:259	(-76.68, 18.88, -16.39)
6:49423923	rs375054307	I>V	B:261	(-71.28, 19.95, -13.96)
6:49423898		A>V	B:269	(-61.16, 32.91, -16.59)
6:49423880		L>R	B:275	(-61.09, 28.21, -7.52)
6:49423878		E>Q	B:276	(-61.77, 24.17, -11.91)
6:49423868	rs2228282	Y>C	B:279	(-65.91, 27.87, -7.08)
6:49423838		R>T	B:289	(-79.32, 21.50, -3.38)
6:49423839		R>G	B:289	(-79.32, 21.50, -3.38)
6:49423830		L>F	B:292	(-84.22, 16.63, -4.74)
6:49423825		Q>H	B:293	(-87.07, 20.03, -6.39)
6:49423826	rs138374956	Q>R	B:293	(-87.07, 20.03, -6.39)
6:49423814	rs547709692	T>I	B:297	(-84.46, 10.42, -6.43)
6:49423793		R>K	B:304	(-78.32, 11.24, -16.30)
6:49421450		I>V	B:311	(-56.32, 20.07, -18.61)
6:49421444		M>L	B:313	(-49.08, 23.41, -18.85)
6:49421434		Y>C	B:316	(-46.71, 16.89, -11.41)
6:49421431	rs184829210	M>T	B:317	(-52.16, 20.51, -9.68)
6:49421432		M>V	B:317	(-52.16, 20.51, -9.68)
6:49421411	COSM742690 CM050678	A>S	B:324	(-59.55, 14.66, -5.83)
6:49421404		R>K	B:326	(-62.28, 10.71, -9.33)
6:49421389		H>R	B:331	(-67.41, 13.11, 1.31)
6:49421381		E>K	B:334	(-71.97, 9.00, 1.10)
6:49421376		K>N	B:335	(-72.20, 13.76, 4.47)
6:49421373	rs150095448	M>I	B:336	(-75.16, 16.16, 1.27)
6:49421375		M>V	B:336	(-75.16, 16.16, 1.27)
6:49421350	COSM124580 CM050682 CM071015	S>C	B:344	(-74.76, 7.86, -7.58)
6:49421345	rs140775584	L>I	B:346	(-69.49, 7.68, -10.29)
6:49421326		Q>R	B:352	(-61.11, 21.21, -23.63)
6:49421305		T>I	B:359	(-49.54, 30.71, -28.13)
6:49419420	rs563776413 CM074361	Y>S	B:364	(-46.22, 24.82, -35.67)
6:49419418		N>D	B:365	(-44.46, 25.61, -29.49)
6:49419406		R>C	B:369	(-47.80, 24.43, -25.16)
6:49419403	rs368790885 CM060373	T>P	B:370	(-51.82, 19.89, -26.44)
6:49419395		I>M	B:372	(-47.88, 18.05, -21.78)
6:49419396	rs150968643	I>T	B:372	(-47.88, 18.05, -21.78)
6:49419397		I>V	B:372	(-47.88, 18.05, -21.78)
6:49419386	rs148091558	M>I	B:375	(-50.02, 12.76, -21.03)
6:49419375		F>C	B:379	(-51.27, 9.96, -16.68)
6:49419349		N>D	B:388	(-56.99, 22.31, -28.52)
6:49419327		G>D	B:395	(-58.51, 30.48, -35.16)
6:49419321		P>L	B:397	(-59.23, 24.75, -37.10)
6:49419306		A>G	B:402	(-56.94, 18.76, -36.89)
6:49419303	COSM1080059	R>Q	B:403	(-54.66, 13.93, -39.19)
6:49419291		N>S	B:407	(-53.07, 11.87, -34.59)
6:49419292	rs576536579	N>Y	B:407	(-53.07, 11.87, -34.59)
6:49419289		T>S	B:408	(-52.05, 13.71, -29.96)
6:49419265		S>T	B:416	(-47.56, 4.83, -25.24)
6:49419256	COSM1697348	P>T	B:419	(-53.33, 2.84, -21.99)
6:49419250		V>M	B:421	(-51.61, 0.62, -16.39)
6:49419244		D>H	B:423	(-54.02, 5.01, -11.42)
6:49419241	rs373381232	P>S	B:424	(-50.41, 4.77, -13.44)
6:49419231		G>D	B:427	(-48.35, 5.57, -4.96)
6:49419225	rs201741770	Y>C	B:429	(-43.78, 8.00, -2.45)
6:49419215		E>D	B:432	(-51.31, 9.76, -3.47)
6:49419214	rs375604969	C>R	B:433	(-49.55, 13.91, -1.02)
6:49419202		D>N	B:437	(-52.86, 18.66, -0.25)
6:49416629		E>D	B:448	(-66.23, 28.56, 3.05)
6:49416622		E>K	B:451	(-71.29, 28.46, 6.25)
6:49416618		M>K	B:452	(-72.24, 31.25, 1.89)
6:49416615		G>D	B:453	(-76.13, 28.61, 0.90)
6:49416582		P>L	B:464	(-67.24, 33.46, -7.01)
6:49416573	rs147737629	R>Q	B:467	(-62.61, 34.90, -4.42)
6:49416568	rs200850870	E>K	B:469	(-62.16, 38.63, -11.63)
6:49416564		E>G	B:470	(-58.56, 37.99, -7.24)
6:49416558		A>V	B:472	(-56.29, 36.52, -13.65)
6:49416556	rs188766510	A>S	B:473	(-54.52, 39.20, -12.13)
6:49416552	rs368746965	R>Q	B:474	(-53.22, 36.49, -8.41)
6:49416537		I>T	B:479	(-46.94, 36.33, -17.49)
6:49415496		S>P	B:483	(-42.29, 34.64, -12.58)
6:49415483		V>A	B:487	(-41.96, 29.45, -24.77)
6:49415477		V>E	B:489	(-44.40, 35.15, -25.32)
6:49415471		K>T	B:491	(-37.84, 33.33, -22.33)
6:49415450	rs377604600	D>G	B:498	(-44.37, 32.88, -39.54)
6:49415448	rs2229385	A>T	B:499	(-47.51, 35.20, -42.41)
6:49415442		E>Q	B:501	(-53.74, 34.17, -44.59)
6:49415439		V>I	B:502	(-57.27, 35.85, -43.37)
6:49415424		N>D	B:507	(-72.21, 37.47, -40.94)
6:49415411		R>Q	B:511	(-77.22, 39.23, -41.42)
6:49415407		N>K	B:512	(-79.14, 38.41, -45.28)
6:49415391		L>V	B:518	(-87.57, 35.10, -39.57)
6:49415384	rs199655896	K>T	B:520	(-91.66, 33.32, -44.11)
6:49412464		K>Q	B:522	(-94.10, 35.02, -39.77)
6:49412458	rs372988725	S>G	B:524	(-96.97, 31.20, -42.65)
6:49412445		A>V	B:528	(-103.09, 33.35, -32.84)
6:49412433	rs1141321	R>H	B:532	(-103.85, 31.27, -27.22)
6:49412434		R>C	B:532	(-103.85, 31.27, -27.22)
6:49412430	rs139765234	C>Y	B:533	(-98.20, 30.02, -26.79)
6:49412431		C>R	B:533	(-98.20, 30.02, -26.79)
6:49412425		A>P	B:535	(-99.16, 33.97, -23.14)
6:49412421	rs369902876	A>V	B:536	(-98.72, 30.78, -21.63)
6:49412413		E>K	B:539	(-99.48, 33.12, -16.57)
6:49412406		A>V	B:541	(-93.58, 32.73, -15.15)
6:49412403		A>V	B:542	(-96.10, 34.25, -13.15)
6:49412400		S>N	B:543	(-97.90, 31.48, -11.72)
6:49412398	rs78150750	G>R	B:544	(-96.02, 28.50, -11.60)
6:49412379		A>V	B:550	(-93.95, 22.11, -22.05)
6:49412365		A>T	B:555	(-94.28, 27.41, -29.07)
6:49412358	COSM3703022	R>Q	B:557	(-95.70, 21.91, -31.69)
6:49412356		A>S	B:558	(-96.24, 27.39, -33.37)
6:49409643		F>S	B:573	(-88.34, 35.38, -15.10)
6:49409628		A>V	B:578	(-74.11, 42.86, -13.14)
6:49409619		R>Q	B:581	(-67.01, 44.16, -8.18)
6:49409610		S>T	B:584	(-57.93, 46.08, -6.09)
6:49409599	rs140727018	R>C	B:588	(-48.59, 47.52, -7.23)
6:49409584	rs148285323	E>Q	B:593	(-41.07, 44.85, -6.94)
6:49409579		S>R	B:594	(-40.62, 47.24, -10.22)
6:49409575	rs545334525 CD060622	E>K	B:596	(-41.47, 48.67, -15.35)
6:49409572		I>L	B:597	(-44.62, 49.57, -11.69)
6:49409560	rs201888226	I>V	B:601	(-47.03, 55.32, -10.66)
6:49408065		V>F	B:604	(-49.78, 58.81, -13.65)
6:49408061		H>R	B:605	(-48.84, 60.86, -9.93)
6:49408062		H>Y	B:605	(-48.84, 60.86, -9.93)
6:49408058		K>R	B:606	(-47.07, 64.10, -13.93)
6:49408046	COSM1292337	R>H	B:610	(-50.43, 68.71, -15.67)
6:49408038	rs573727541 COSM3628247	R>C	B:613	(-58.59, 64.41, -15.31)
6:49408029		R>C	B:616	(-61.71, 58.90, -17.02)
6:49408010	rs201536536	M>T	B:622	(-68.19, 46.10, -28.71)
6:49408008	rs121918254	G>R	B:623	(-71.40, 42.80, -28.19)
6:49408004		Q>R	B:624	(-73.92, 39.77, -27.37)
6:49407995	rs372486357 CM002070	H>R	B:627	(-65.17, 35.20, -24.07)
6:49407989		R>K	B:629	(-58.66, 36.05, -18.45)
6:49407986	rs143023066	G>E	B:630	(-58.57, 40.70, -20.40)
6:49407974		I>S	B:634	(-56.10, 45.69, -19.02)
6:49407975		I>V	B:634	(-56.10, 45.69, -19.02)
6:49407969	rs569669261	T>A	B:636	(-57.02, 45.78, -12.49)
6:49407966		G>R	B:637	(-53.91, 47.38, -13.87)
6:49407932		G>D	B:648	(-68.12, 48.23, -19.51)
6:49407933	COSM1080055	G>S	B:648	(-68.12, 48.23, -19.51)
6:49403329	rs567485663	R>H	B:655	(-73.81, 54.05, -29.48)
6:49403330	rs541001298	R>C	B:655	(-73.81, 54.05, -29.48)
6:49403302	rs137958217	A>V	B:664	(-67.13, 60.12, -18.72)
6:49403296		V>A	B:666	(-62.93, 59.40, -21.54)
6:49403297		V>L	B:666	(-62.93, 59.40, -21.54)
6:49403284		G>A	B:670	(-60.92, 50.20, -24.84)
6:49403282	rs8589	I>V	B:671	(-61.86, 48.04, -27.63)
6:49403278		S>N	B:672	(-61.82, 43.63, -26.94)
6:49403270	rs367850243 COSM1080054	A>T	B:675	(-63.34, 37.75, -34.77)
6:49403267	rs147715336	A>T	B:676	(-63.59, 40.45, -37.23)
6:49403222		S>A	B:691	(-71.76, 61.81, -33.95)
6:49403215		G>V	B:693	(-68.26, 65.28, -30.67)
6:49403212		R>Q	B:694	(-65.32, 64.02, -27.66)
6:49403213		R>W	B:694	(-65.32, 64.02, -27.66)
6:49403209	rs561197473	P>L	B:695	(-63.30, 63.44, -32.59)
6:49403206		D>A	B:696	(-60.93, 64.07, -29.06)
6:49403200		L>H	B:698	(-57.90, 58.28, -28.29)
6:49403194	rs140600746	M>K	B:700	(-56.79, 52.12, -27.79)
6:49403186	rs121918255	G>R	B:703	(-57.21, 40.87, -29.40)
6:49403179		I>T	B:705	(-56.22, 41.82, -34.29)
6:49399548		V>I	B:716	(-60.27, 53.89, -39.27)
6:49399544	rs121918252	G>V	B:717	(-58.33, 55.90, -36.17)
6:49399545	COSM3628244	G>R	B:717	(-58.33, 55.90, -36.17)
6:49399536		N>D	B:720	(-52.34, 51.60, -30.48)
6:49399532		V>A	B:721	(-52.86, 47.88, -31.54)
6:49399526		G>D	B:723	(-51.02, 42.48, -28.94)
6:49399518		T>S	B:726	(-49.19, 43.08, -24.30)
6:49399503		A>T	B:731	(-49.41, 49.70, -22.23)
6:49399499		A>D	B:732	(-49.75, 52.26, -19.82)
6:49399488		L>F	B:736	(-49.76, 58.33, -20.74)
6:49399485		D>H	B:737	(-47.15, 58.45, -24.62)

3BIC.B | MUT.

3BIC.B | MUT

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
6:49426979	COSM1754856	I>M	B:67	(-50.75, 23.66, -2.61)
6:49419405	COSM336255	R>P	B:369	(-47.80, 24.43, -25.16)
6:49419381	COSM3662608	A>E	B:377	(-56.00, 13.70, -18.85)
6:49419303	COSM1080059	R>Q	B:403	(-54.66, 13.93, -39.19)
6:49416630	COSM1634836	E>G	B:448	(-66.23, 28.56, 3.05)
6:49409556	COSM3662607	K>R	B:602	(-44.53, 58.87, -11.85)
6:49408046	COSM1292337	R>H	B:610	(-50.43, 68.71, -15.67)
6:49403270	COSM1080054	A>T	B:675	(-63.34, 37.75, -34.77)
6:49403260	COSM742693	H>R	B:678	(-61.26, 44.06, -36.42)