4F0X.H | MLYCD

General Structure Information

PDB ID	4f0x
HGNC Gene Label(s)	MLYCD
Structure Name	crystal structure of human malonyl-coa decarboxylase (peroxisomal isoform)
Resolution	3.29Å
Reference	AUTH D.APARICIO,R.PEREZ-LUQUE,X.CARPENA,M.DIAZ,J.C.FERRER,AUTH 2 P.C.LOEWEN,I.FITATITL STRUCTURAL ASYMMETRY AND DISULFIDE BRIDGES AMONG SUBUNITSTITL 2 MODULATE THE ACTIVITY OF HUMAN MALONYL-COA DECARBOXYLASE.REF J.BIOL.CHEM. V. 288 11907 2013REFN ISSN 0021-9258PMID 23482565DOI 10.1074/JBC.M112.443846

Variant Set Distributions

ExAC Variants

Number Of Residues	445
Number Of SNVs	146
Number Of Permutations	41991
Optimal Distance Threshold	14.0
K Statistic	0.104
p-value	0.005

COSMIC

Number Of Residues	445
Number Of SNVs	3
Number Of Permutations	160
Optimal Distance Threshold	18.0
K Statistic	0.667
p-value	0.108

Ripley’s K Analysis Plots

ExACCOSMIC

Variant Set Comparisons

Cosmic vs. ExAC

Number Of ExAC SNVs	146
Number Of COSMIC SNVs	3
Optimal Distance Threshold	26.0
K Statistic	0.62
p-value	0.163

Pathogenic Proximity Analysis

COSMIC PathProx Analysis

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
16:83932906		A>T	H:53	(-6.80, 73.90, 35.50)
16:83932930		P>A	H:61	(-10.15, 63.26, 34.32)
16:83932936		P>A	H:63	(-13.03, 60.74, 38.09)
16:83932942		E>K	H:65	(-15.74, 56.47, 33.34)
16:83932946		G>D	H:66	(-18.26, 57.95, 36.90)
16:83932951		C>G	H:68	(-20.92, 60.71, 33.82)
16:83932955	rs200579941 CM033648	A>V	H:69	(-22.73, 57.28, 34.95)
16:83932962		F>L	H:71	(-26.26, 63.08, 34.59)
16:83932978		G>W	H:77	(-34.77, 57.48, 36.68)
16:83932993		A>P	H:82	(-40.84, 67.78, 34.79)
16:83933014		G>S	H:89	(-31.97, 74.00, 34.62)
16:83933018		R>L	H:90	(-31.65, 72.73, 39.34)
16:83933075		V>E	H:109	(-6.35, 90.76, 27.41)
16:83933090		Q>R	H:114	(-2.61, 99.07, 28.99)
16:83933104		A>S	H:119	(2.59, 87.51, 21.02)
16:83933121		Q>H	H:124	(-0.97, 82.03, 27.21)
16:83933138		R>H	H:130	(-10.05, 80.89, 23.53)
16:83933143		A>S	H:132	(-13.02, 80.55, 30.62)
16:83933149	rs570734130	V>L	H:134	(-15.77, 76.61, 27.89)
16:83933153		P>R	H:135	(-19.25, 75.95, 29.09)
16:83933159		Y>C	H:137	(-23.10, 73.23, 29.92)
16:83933161		R>G	H:138	(-18.31, 70.95, 25.44)
16:83933164		G>S	H:139	(-17.85, 67.94, 29.78)
16:83933167		L>F	H:140	(-21.49, 66.32, 31.38)
16:83933179		I>V	H:144	(-21.90, 61.48, 28.53)
16:83933191		D>N	H:148	(-21.40, 51.59, 26.48)
16:83933192		D>G	H:148	(-21.40, 51.59, 26.48)
16:83933194		G>S	H:149	(-24.66, 55.04, 25.41)
16:83933195		G>D	H:149	(-24.66, 55.04, 25.41)
16:83933200		V>L	H:151	(-24.34, 59.55, 21.51)
16:83933212		V>L	H:155	(-30.19, 62.34, 21.16)
16:83933216		Q>L	H:156	(-33.87, 61.21, 24.67)
16:83933231		L>P	H:161	(-33.81, 70.84, 26.13)
16:83933242		Q>K	H:165	(-37.58, 75.17, 25.29)
16:83933246		A>V	H:166	(-42.40, 73.64, 23.77)
16:83933261		E>G	H:171	(-38.66, 80.39, 30.27)
16:83940595		M>V	H:178	(-27.57, 73.93, 27.58)
16:83940604	rs147617160	V>M	H:181	(-23.48, 73.81, 23.35)
16:83940614	rs200783818	G>E	H:184	(-22.88, 71.27, 17.97)
16:83940619		L>F	H:186	(-25.30, 66.32, 18.38)
16:83940640	rs369616872 COSM1380137	G>R	H:193	(-19.07, 60.74, 7.92)
16:83940655	rs201780465	E>K	H:198	(-28.35, 51.33, 5.25)
16:83940658		R>W	H:199	(-31.22, 49.46, -1.49)
16:83940659		R>Q	H:199	(-31.22, 49.46, -1.49)
16:83940674		S>L	H:204	(-34.32, 43.50, 3.67)
16:83940676		P>S	H:205	(-34.60, 42.47, 7.17)
16:83940677		P>L	H:205	(-34.60, 42.47, 7.17)
16:83940686		V>G	H:208	(-35.75, 46.91, 8.56)
16:83940693		Q>H	H:210	(-41.89, 46.72, 11.65)
16:83940695		K>T	H:211	(-37.54, 49.91, 12.31)
16:83940700	rs552425982	S>C	H:213	(-43.61, 51.41, 8.18)
16:83941732		A>S	H:215	(-41.09, 56.08, 10.47)
16:83941738	rs368843501	A>T	H:217	(-44.09, 60.93, 7.77)
16:83941750		V>L	H:221	(-47.65, 52.40, 4.19)
16:83941756	rs188078575	N>Y	H:223	(-50.84, 47.17, 2.08)
16:83941757	rs367804337	N>I	H:223	(-50.84, 47.17, 2.08)
16:83941764		M>I	H:225	(-49.70, 43.71, -0.82)
16:83941772		K>R	H:228	(-43.30, 43.85, -2.63)
16:83941775	rs142117752	R>H	H:229	(-46.45, 48.54, -4.50)
16:83941778		R>H	H:230	(-43.92, 52.54, -1.14)
16:83941780		V>I	H:231	(-38.90, 48.24, -2.07)
16:83941792	rs369427189	R>G	H:235	(-40.71, 53.01, -7.17)
16:83941793		R>K	H:235	(-40.71, 53.01, -7.17)
16:83941811	rs373660011	S>C	H:241	(-27.04, 54.93, 9.79)
16:83941813		H>D	H:242	(-24.09, 56.85, 13.72)
16:83941820	rs375719723	S>L	H:244	(-21.97, 53.23, 15.89)
16:83941837		L>V	H:250	(-31.41, 58.52, 11.71)
16:83941847	rs373601041	L>W	H:253	(-34.67, 58.88, 1.75)
16:83941852	rs377566911 COSM1380138	V>M	H:255	(-36.82, 57.40, -4.81)
16:83941870		I>V	H:261	(-40.45, 66.34, -13.23)
16:83941876	rs570550620	S>G	H:263	(-47.35, 66.09, -10.80)
16:83941879		N>D	H:264	(-49.90, 62.91, -8.98)
16:83945826		I>V	H:268	(-45.92, 57.49, -7.39)
16:83945829	rs371367725 COSM1189329	V>M	H:269	(-48.41, 55.03, -4.35)
16:83945844		P>A	H:274	(-45.05, 45.28, -15.43)
16:83945853	rs201103147	T>A	H:277	(-36.45, 43.92, -14.53)
16:83945874	rs62640903	T>A	H:284	(-35.19, 60.62, -17.41)
16:83945881	rs376453144 COSM974299	A>V	H:286	(-35.23, 61.40, -9.76)
16:83945904	rs200365808 COSM4063216	T>A	H:294	(-36.64, 58.73, 12.95)
16:83945905		T>S	H:294	(-36.64, 58.73, 12.95)
16:83945911	rs199761233	Q>P	H:296	(-37.92, 64.39, 16.53)
16:83945916	rs563907654	L>V	H:298	(-31.16, 64.91, 15.40)
16:83945922		G>R	H:300	(-31.60, 70.91, 12.78)
16:83945923		G>V	H:300	(-31.60, 70.91, 12.78)
16:83945925	rs199656023	V>L	H:301	(-28.37, 69.31, 13.60)
16:83945931		L>M	H:303	(-27.61, 71.20, 5.91)
16:83945935		G>V	H:304	(-29.28, 67.92, 3.80)
16:83945937	rs200745228	T>S	H:305	(-27.16, 68.67, 0.88)
16:83945946		I>V	H:308	(-30.42, 64.53, -1.50)
16:83945949	rs149926091	K>Q	H:309	(-25.57, 66.06, -3.23)
16:83948605		I>M	H:331	(-47.89, 72.58, 0.79)
16:83948607	rs370002912	P>R	H:332	(-47.67, 71.45, 5.14)
16:83948609		G>S	H:333	(-50.30, 74.93, 6.28)
16:83948616	rs76060070	T>N	H:335	(-55.82, 74.99, 4.11)
16:83948619	rs76841036	K>R	H:336	(-54.60, 75.53, 9.01)
16:83948625	rs374073138	L>P	H:338	(-56.66, 80.27, 2.96)
16:83948634		L>R	H:341	(-56.15, 85.18, 5.74)
16:83948640		N>S	H:343	(-62.05, 84.89, 8.52)
16:83948679		T>K	H:356	(-61.18, 88.73, -8.97)
16:83948682	rs577969223	D>G	H:357	(-64.94, 91.19, -9.00)
16:83948697		E>G	H:362	(-67.28, 81.93, -11.32)
16:83948699		I>V	H:363	(-67.05, 81.06, -6.47)
16:83948700		I>N	H:363	(-67.05, 81.06, -6.47)
16:83948709	rs376504760	I>N	H:366	(-70.74, 77.49, -8.64)
16:83948721		P>L	H:370	(-72.25, 85.06, -0.30)
16:83948729	COSM1197280	E>K	H:373	(-69.81, 82.93, 5.31)
16:83948731		E>D	H:373	(-69.81, 82.93, 5.31)
16:83948733		T>I	H:374	(-69.12, 80.31, 0.78)
16:83948736		L>P	H:375	(-64.89, 79.85, 0.09)
16:83948745		L>H	H:378	(-66.66, 74.87, 0.98)
16:83948747		L>F	H:379	(-62.11, 75.51, 1.74)
16:83948763		W>L	H:384	(-62.84, 71.73, -2.87)
16:83948786	rs530627828	R>W	H:392	(-63.05, 73.52, -14.09)
16:83948798		T>P	H:396	(-56.42, 80.65, -11.14)
16:83948801		P>T	H:397	(-57.28, 81.48, -7.48)
16:83948802		P>L	H:397	(-57.28, 81.48, -7.48)
16:83948805		L>P	H:398	(-56.20, 78.29, -4.75)
16:83948811	rs374610037	R>T	H:400	(-53.53, 84.00, -7.18)
16:83948812		R>S	H:400	(-53.53, 84.00, -7.18)
16:83948814		L>P	H:401	(-53.44, 82.34, -2.70)
16:83948816		C>R	H:402	(-49.75, 78.83, -2.89)
16:83948819	rs569549800	A>S	H:403	(-47.34, 81.22, -4.58)
16:83948826		Y>F	H:405	(-47.84, 79.51, 2.46)
16:83948828		L>V	H:406	(-44.40, 78.90, -0.65)
16:83948832	rs375649018	Y>C	H:407	(-41.25, 84.11, -3.39)
16:83948834		G>R	H:408	(-43.90, 85.71, 0.61)
16:83948849	rs374608119	G>S	H:413	(-37.38, 85.69, 6.69)
16:83948852		Y>N	H:414	(-34.94, 82.33, 7.11)
16:83948853	rs368099850	Y>C	H:414	(-34.94, 82.33, 7.11)
16:83948861		N>Y	H:417	(-43.73, 75.87, 4.72)
16:83948867		V>L	H:419	(-41.33, 71.53, 3.61)
16:83948888		N>D	H:426	(-30.84, 71.86, 1.17)
16:83948891	rs377271580	G>R	H:427	(-30.79, 74.56, -2.78)
16:83948895	rs371429195	A>V	H:428	(-33.70, 74.01, -3.82)
16:83948900	rs375981938	L>V	H:430	(-40.01, 77.07, -5.72)
16:83948906	rs35124955	R>C	H:432	(-43.94, 72.01, -11.20)
16:83948907	rs201973830	R>H	H:432	(-43.94, 72.01, -11.20)
16:83948912		N>D	H:434	(-48.42, 70.86, -8.62)
16:83948913		N>T	H:434	(-48.42, 70.86, -8.62)
16:83948922		A>V	H:437	(-51.66, 66.51, -6.66)
16:83948940	rs200278015	G>A	H:443	(-54.50, 66.79, 1.17)
16:83948942		I>V	H:444	(-57.95, 68.15, -0.08)
16:83948948	rs377075332	G>S	H:446	(-53.91, 70.77, 4.18)
16:83948952	rs552095283 COSM3889077	S>F	H:447	(-52.94, 71.53, 0.61)
16:83948972		Y>H	H:454	(-39.58, 72.10, -3.22)
16:83948976	COSM4063219	R>H	H:455	(-35.22, 70.88, -10.54)
16:83948985		L>P	H:458	(-26.50, 68.79, -9.31)
16:83948994		T>M	H:461	(-26.74, 73.34, -4.45)
16:83949003		N>S	H:464	(-28.97, 78.28, -4.57)
16:83949008		T>A	H:466	(-25.43, 81.13, 0.38)
16:83949012		S>C	H:467	(-28.59, 82.90, -1.34)
16:83949015		Y>S	H:468	(-32.96, 80.42, 2.23)
16:83949020	rs142671250	G>S	H:470	(-27.80, 84.89, 4.25)
16:83949021		G>V	H:470	(-27.80, 84.89, 4.25)
16:83949024	COSM3512879	S>C	H:471	(-29.47, 86.74, 1.70)
16:83949027		K>T	H:472	(-32.90, 85.91, 4.38)
16:83949029		I>V	H:473	(-32.56, 85.02, -1.71)
16:83949032	rs375935118	I>V	H:474	(-36.57, 82.20, -2.62)
16:83949044		E>K	H:478	(-40.62, 81.68, -15.63)
16:83949045	rs200078965	E>G	H:478	(-40.62, 81.68, -15.63)
16:83949049	rs374909342	Q>H	H:479	(-45.04, 78.20, -12.50)
16:83949058		S>R	H:482	(-46.25, 84.30, -12.71)
16:83949082		N>K	H:490	(-54.63, 90.79, -5.46)

4F0X.H | MLYCD.

4F0X.H | MLYCD

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

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
16:83941878	COSM4988864	S>R	H:263	(-47.35, 66.09, -10.80)
16:83945829	COSM1189329	V>M	H:269	(-48.41, 55.03, -4.35)
16:83948787	COSM3717111	R>L	H:392	(-63.05, 73.52, -14.09)