4AH6.D | DARS2

General Structure Information

PDB ID	4ah6
HGNC Gene Label(s)	DARS2
Structure Name	human mitochondrial aspartyl-trna synthetase
Resolution	3.7Å
Reference	AUTH E.ENNIFAR,C.FLORENTZ,A.GAUDRY,B.LORBER,A.NEUENFELDT,AUTH 2 C.SAUTER,M.SISSLERTITL THERMODYNAMIC PROPERTIES DISTINGUISH HUMAN MITOCHONDRIALTITL 2 ASPARTYL-TRNA SYNTHETASE FROM BACTERIAL HOMOLOG WITH SAMETITL 3 3D ARCHITECTUREREF NUCLEIC ACIDS RES. V. 41 2698 2013REFN ISSN 0305-1048PMID 23275545DOI 10.1093/NAR/GKS1322

Variant Set Distributions

ExAC Variants

Number Of Residues	589
Number Of SNVs	138
Number Of Permutations	39886
Optimal Distance Threshold	30.0
K Statistic	0.369
p-value	0.249

ClinVar

Number Of Residues	589
Number Of SNVs	7
Number Of Permutations	2141
Optimal Distance Threshold	26.0
K Statistic	0.571
p-value	0.114

COSMIC

Number Of Residues	589
Number Of SNVs	9
Number Of Permutations	3878
Optimal Distance Threshold	9.0
K Statistic	0.083
p-value	0.784

Ripley’s K Analysis Plots

ExACClinVarCOSMIC

Variant Set Comparisons

ClinVar vs. ExAC

Number Of ExAC SNVs	138
Number Of ClinVar SNVs	6
Optimal Distance Threshold	26.0
K Statistic	0.253
p-value	0.168

Cosmic vs. ExAC

Number Of ExAC SNVs	138
Number Of COSMIC SNVs	8
Optimal Distance Threshold	9.0
K Statistic	0.087
p-value	0.215

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
1:173794491		P>T	D:42	(40.81, -46.98, 143.22)
1:173795852		N>S	D:52	(42.27, -58.60, 139.23)
1:173795857		C>R	D:54	(39.09, -58.20, 133.00)
1:173795869	rs375700548 COSM899790	R>G	D:58	(48.79, -53.46, 132.65)
1:173795870		R>H	D:58	(48.79, -53.46, 132.65)
1:173795873	COSM2075683	S>L	D:59	(53.08, -57.20, 132.66)
1:173795897	rs202232688	T>I	D:67	(39.59, -65.46, 139.92)
1:173795917	rs547544541	Y>N	D:74	(35.90, -63.16, 119.68)
1:173797503	rs149598381	D>G	D:87	(37.59, -51.86, 132.54)
1:173797533	rs376385086 COSM1196284	D>G	D:97	(44.31, -81.75, 128.48)
1:173799798	rs376537017	S>T	D:99	(42.54, -82.47, 132.87)
1:173799799	COSM1336370	S>L	D:99	(42.54, -82.47, 132.87)
1:173799831		A>T	D:110	(29.12, -70.72, 125.94)
1:173799844	rs566829104	S>C	D:114	(27.36, -65.30, 128.49)
1:173799850		V>A	D:116	(32.07, -66.73, 132.58)
1:173799876		R>C	D:125	(49.39, -62.50, 124.11)
1:173799877		R>H	D:125	(49.39, -62.50, 124.11)
1:173799886		G>E	D:128	(54.18, -61.76, 118.62)
1:173800682		T>A	D:136	(45.18, -56.97, 127.93)
1:173800699		I>M	D:141	(44.34, -66.15, 131.28)
1:173800718		L>F	D:148	(27.86, -71.04, 133.30)
1:173800731	rs121918208	C>F	D:152	(22.43, -66.17, 126.35)
1:173800759	rs373024912	N>K	D:161	(31.28, -51.89, 116.71)
1:173800760		F>V	D:162	(30.89, -49.55, 120.94)
1:173800763	rs199930349	V>M	D:163	(25.79, -51.20, 118.45)
1:173802524		A>G	D:168	(14.62, -47.96, 118.94)
1:173802529		R>W	D:170	(21.07, -47.63, 121.37)
1:173802541		R>C	D:174	(19.75, -48.24, 126.81)
1:173802556		R>C	D:179	(26.42, -55.60, 128.20)
1:173802557	rs121918210	R>H	D:179	(26.42, -55.60, 128.20)
1:173802584	rs182811621	R>Q	D:188	(31.84, -45.51, 134.74)
1:173802587		L>Q	D:189	(32.40, -38.94, 132.64)
1:173802601	rs186723843	V>I	D:194	(29.01, -35.10, 139.52)
1:173802607		K>Q	D:196	(35.43, -34.26, 140.62)
1:173802608	rs35515638	K>R	D:196	(35.43, -34.26, 140.62)
1:173802611		M>T	D:197	(31.02, -31.01, 140.78)
1:173802614		R>Q	D:198	(28.44, -33.77, 145.21)
1:173802619		Y>H	D:200	(34.76, -26.59, 144.19)
1:173802623		L>P	D:201	(30.67, -27.42, 146.13)
1:173802635		H>R	D:205	(34.92, -23.91, 148.37)
1:173803628		T>A	D:212	(14.24, -29.50, 147.77)
1:173803638		L>W	D:215	(5.57, -33.54, 146.28)
1:173806079		G>V	D:222	(7.20, -20.01, 133.13)
1:173806127	COSM3710433	S>F	D:238	(3.03, -29.85, 141.45)
1:173806130		L>P	D:239	(6.22, -32.14, 139.89)
1:173806133		P>R	D:240	(9.22, -29.30, 140.49)
1:173806152		F>L	D:246	(12.29, -24.53, 148.11)
1:173806156		Q>K	D:248	(14.74, -17.10, 147.81)
1:173806174	COSM297799	G>S	D:254	(20.89, -19.70, 156.29)
1:173806175		G>D	D:254	(20.89, -19.70, 156.29)
1:173807341		A>S	D:262	(17.80, -31.65, 141.03)
1:173807345	rs121918207	R>Q	D:263	(15.63, -35.94, 139.29)
1:173807354	COSM4025222	R>Q	D:266	(11.19, -29.76, 130.64)
1:173807356	rs573387261	D>N	D:267	(5.04, -30.16, 130.38)
1:173807363		G>D	D:269	(3.84, -29.22, 124.32)
1:173807366		S>L	D:270	(5.42, -26.85, 122.25)
1:173807376		D>E	D:273	(12.41, -33.71, 121.53)
1:173807381		Q>L	D:275	(14.12, -35.83, 128.16)
1:173807395		Q>E	D:280	(19.32, -28.60, 137.25)
1:173808545		Q>P	D:294	(31.50, -14.82, 137.17)
1:173808554		I>T	D:297	(30.79, -21.94, 138.10)
1:173808581		P>R	D:306	(37.22, -34.67, 132.80)
1:173808585		N>K	D:307	(42.09, -35.29, 133.61)
1:173808608		P>L	D:315	(39.43, -16.61, 134.09)
1:173808614	rs373907765	P>R	D:317	(35.65, -15.02, 128.66)
1:173808653		T>N	D:330	(23.36, -15.27, 119.46)
1:173808661		P>A	D:333	(28.16, -17.67, 121.15)
1:173808671		R>H	D:336	(34.40, -23.51, 118.81)
1:173808677	rs141298312	G>E	D:338	(35.87, -16.25, 115.14)
1:173810011	rs200537352	D>G	D:343	(29.87, -1.62, 111.93)
1:173810022		V>M	D:347	(33.50, 3.37, 105.23)
1:173810031	rs572878883	N>D	D:350	(31.08, 8.64, 101.29)
1:173810041	rs535513181	I>T	D:353	(26.25, 2.19, 95.92)
1:173810047		F>S	D:355	(22.66, -2.41, 98.83)
1:173810071		P>R	D:363	(17.08, 5.89, 111.66)
1:173810079		T>S	D:366	(23.55, -0.64, 109.51)
1:173810101	rs369412405	P>H	D:373	(38.87, -17.25, 107.29)
1:173814380	rs549700561	R>M	D:381	(34.41, -19.28, 93.07)
1:173814410		A>V	D:391	(18.92, -15.20, 101.88)
1:173814419		H>P	D:394	(17.46, -15.40, 107.62)
1:173814425		N>S	D:396	(14.54, -11.96, 102.06)
1:173819483	COSM899797	L>V	D:404	(39.56, -7.60, 99.38)
1:173819489		A>T	D:406	(41.80, -13.44, 96.64)
1:173819493		N>S	D:407	(40.13, -15.07, 93.75)
1:173819497		R>S	D:408	(42.06, -8.46, 93.08)
1:173819504	rs531672172	N>D	D:411	(35.16, -12.75, 91.78)
1:173819513		V>L	D:414	(28.58, -4.98, 92.90)
1:173819514	rs376973272	V>A	D:414	(28.58, -4.98, 92.90)
1:173819519	rs138154457	N>D	D:416	(35.14, -4.83, 91.63)
1:173819527		I>M	D:418	(33.31, -1.67, 97.16)
1:173819528		M>V	D:419	(37.96, -3.82, 95.45)
1:173819538		Q>R	D:422	(37.16, 1.88, 100.20)
1:173819559		L>Q	D:429	(37.92, -2.07, 109.47)
1:173819568		T>I	D:432	(41.79, -9.08, 105.79)
1:173819578	rs150642385	E>D	D:435	(43.70, -16.88, 100.58)
1:173819616		A>V	D:448	(21.94, -7.95, 110.12)
1:173822491		S>C	D:450	(20.51, -12.37, 112.84)
1:173822502		K>E	D:454	(21.88, -17.77, 111.43)
1:173822512		L>P	D:457	(26.70, -21.00, 111.99)
1:173822517		C>S	D:459	(30.58, -20.31, 106.94)
1:173822535		T>A	D:465	(32.56, -29.36, 104.38)
1:173822563	rs201652519	T>I	D:474	(38.92, -31.45, 121.19)
1:173822575		F>S	D:478	(33.49, -22.37, 128.84)
1:173822583		V>M	D:481	(26.22, -13.65, 128.93)
1:173822591		D>E	D:483	(24.10, -6.82, 131.62)
1:173822623		P>R	D:494	(2.53, -4.92, 123.95)
1:173822638	rs146122206	S>W	D:499	(9.64, -12.23, 133.39)
1:173822667		P>S	D:509	(22.37, -0.92, 139.62)
1:173822668		P>H	D:509	(22.37, -0.92, 139.62)
1:173822688		Y>N	D:516	(9.35, 2.62, 138.96)
1:173822694		E>K	D:518	(11.51, 4.08, 129.98)
1:173822697	COSM899800	P>S	D:519	(9.77, -0.31, 131.41)
1:173822700	rs201876507	K>Q	D:520	(10.69, -2.89, 128.34)
1:173822936		R>C	D:523	(20.94, -2.68, 132.91)
1:173822946		H>R	D:526	(20.37, -13.37, 134.07)
1:173822957	COSM1185659	V>I	D:530	(27.90, -19.97, 126.92)
1:173822967		G>D	D:533	(26.62, -22.66, 121.73)
1:173822970		N>S	D:534	(25.37, -24.83, 123.91)
1:173822979		G>E	D:537	(23.98, -22.07, 132.22)
1:173822994		R>Q	D:542	(17.84, -14.98, 142.40)
1:173823005		A>T	D:546	(9.94, -6.61, 149.65)
1:173823011	rs149660059	L>M	D:548	(12.11, -3.89, 144.84)
1:173823018		R>H	D:550	(5.61, -4.04, 147.67)
1:173823029	rs147603024	A>T	D:554	(2.11, -5.10, 140.76)
1:173823032		T>A	D:555	(3.44, -4.28, 137.35)
1:173823043		K>N	D:558	(-2.33, -7.57, 141.75)
1:173825808		D>V	D:560	(0.72, -13.94, 142.30)
1:173825819		L>F	D:564	(4.66, -15.31, 145.85)
1:173825820		L>P	D:564	(4.66, -15.31, 145.85)
1:173825823		S>F	D:565	(2.94, -13.74, 150.54)
1:173825855		P>S	D:576	(19.93, -12.43, 152.93)
1:173825858		P>A	D:577	(22.19, -10.52, 150.41)
1:173825861		H>Y	D:578	(19.69, -13.99, 147.67)
1:173826661		D>H	D:586	(21.84, -33.82, 131.18)
1:173826668	rs141483913	L>P	D:588	(28.10, -30.12, 130.73)
1:173826673		C>S	D:590	(26.55, -34.13, 126.02)
1:173826688		S>T	D:595	(27.22, -37.09, 122.53)
1:173826694		S>G	D:597	(21.88, -36.84, 122.31)
1:173826706		V>I	D:601	(24.47, -38.70, 128.89)
1:173826709		I>V	D:602	(20.55, -40.39, 130.17)
1:173826712	rs374139931	A>S	D:603	(20.60, -44.38, 131.77)
1:173826730	rs200670286	R>W	D:609	(5.24, -37.08, 123.40)
1:173826731		R>Q	D:609	(5.24, -37.08, 123.40)
1:173826736		H>Y	D:611	(6.13, -42.88, 125.22)
1:173826749		S>N	D:615	(9.10, -50.21, 129.45)
1:173826753		N>K	D:616	(4.39, -49.71, 128.13)
1:173826767		V>A	D:621	(-5.02, -47.65, 134.54)
1:173826791		Y>C	D:629	(-6.25, -40.85, 143.43)

4AH6.D | DARS2.

4AH6.D | DARS2

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
1:173795830	rs121918209	S>G	D:45	(37.25, -55.36, 141.98)
1:173800731	rs121918208	C>F	D:152	(22.43, -66.17, 126.35)
1:173802557	rs121918210	R>H	D:179	(26.42, -55.60, 128.20)
1:173807345	rs121918207	R>Q	D:263	(15.63, -35.94, 139.29)
1:173826730	rs200670286	R>W	D:609	(5.24, -37.08, 123.40)
1:173826742	rs121918212	L>F	D:613	(11.25, -47.38, 123.81)
1:173826781	rs121918205	L>V	D:626	(-8.99, -42.73, 138.99)
1:173826782	rs121918213	L>Q	D:626	(-8.99, -42.73, 138.99)

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
1:173795869	COSM899790	R>C	D:58	(48.79, -53.46, 132.65)
1:173795873	COSM2075683	S>L	D:59	(53.08, -57.20, 132.66)
1:173803649	COSM3376030	T>A	D:219	(4.88, -21.52, 140.60)
1:173806127	COSM3710433	S>F	D:238	(3.03, -29.85, 141.45)
1:173807338	COSM3705251	V>I	D:261	(21.76, -32.68, 142.44)
1:173819489	COSM3726353	A>T	D:406	(41.80, -13.44, 96.64)
1:173819579	COSM160330	D>H	D:436	(40.38, -13.63, 103.43)
1:173822937	COSM4025223	R>H	D:523	(20.94, -2.68, 132.91)
1:173823017	COSM272567	R>C	D:550	(5.61, -4.04, 147.67)