2NZ2.A | ASS1 – ASTRID

2NZ2.A | ASS1

General Structure Information

PDB ID	2nz2
HGNC Gene Label(s)	ASS1
Structure Name	crystal structure of human argininosuccinate synthase in complex with aspartate and citrulline
Resolution	2.4Å
Reference	AUTH T.KARLBERG,R.COLLINS,S.VAN DEN BERG,A.FLORES,M.HAMMARSTROM,AUTH 2 M.HOGBOM,L.HOLMBERG SCHIAVONE,J.UPPENBERGTITL STRUCTURE OF HUMAN ARGININOSUCCINATE SYNTHETASE.REF ACTA CRYSTALLOGR.,SECT.D V. 64 279 2008REFN ISSN 0907-4449PMID 18323623DOI 10.1107/S0907444907067455

Variant Set Distributions

ExAC Variants

Number Of Residues	402
Number Of SNVs	114
Number Of Permutations	69444
Optimal Distance Threshold	14.0
K Statistic	0.11
p-value	0.454

ClinVar

Number Of Residues	402
Number Of SNVs	21
Number Of Permutations	18835
Optimal Distance Threshold	10.0
K Statistic	0.076
p-value	0.14

COSMIC

Number Of Residues	402
Number Of SNVs	3
Number Of Permutations	76
Optimal Distance Threshold	30.0
K Statistic	0.667
p-value	0.904

Ripley’s K Analysis Plots

ExACClinVarCOSMIC

Variant Set Comparisons

ClinVar vs. ExAC

Number Of ExAC SNVs	114
Number Of ClinVar SNVs	20
Optimal Distance Threshold	10.0
K Statistic	0.024
p-value	0.387

Cosmic vs. ExAC

Pathogenic Proximity Analysis

ClinVar PathProx Analysis

COSMIC PathProx Analysis

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
9:133327634	rs149938546	V>M	A:7	(-13.07, 47.72, 27.16)
9:133327640	rs144999474	L>V	A:9	(-9.62, 45.09, 22.68)
9:133327655	rs121908636	G>S	A:14	(-9.04, 39.61, 13.23)
9:133327668	rs121908643	S>L	A:18	(-13.25, 41.06, 15.26)
9:133327691		E>K	A:26	(-23.47, 41.15, 22.04)
9:133327694	rs543339767	Q>K	A:27	(-21.90, 40.77, 26.83)
9:133327703	COSM1105971	D>N	A:30	(-18.48, 51.02, 25.80)
9:133327706	rs374444560	V>I	A:31	(-15.21, 48.66, 22.75)
9:133329706		Q>H	A:40	(2.56, 45.24, 12.10)
9:133329719		E>K	A:45	(-5.59, 52.84, 7.72)
9:133329728	rs374695792	R>G	A:48	(-10.27, 54.01, 12.55)
9:133329737	rs142350255	A>T	A:51	(-13.68, 48.94, 14.27)
9:133329752		A>T	A:56	(-16.18, 51.11, 18.26)
9:133329755		K>E	A:57	(-16.47, 54.59, 22.23)
9:133333792		F>C	A:60	(-6.83, 54.94, 20.65)
9:133333795		I>T	A:61	(-3.60, 53.61, 15.62)
9:133333803	rs556297791 COSM487122	V>I	A:64	(5.13, 51.20, 19.39)
9:133333819		V>A	A:69	(14.01, 49.00, 18.93)
9:133333837		P>L	A:75	(17.74, 45.43, 26.20)
9:133333842		I>F	A:77	(20.97, 42.81, 21.86)
9:133333854	rs141640176	A>T	A:81	(20.29, 35.47, 25.24)
9:133333855		A>V	A:81	(20.29, 35.47, 25.24)
9:133333858	rs559043503	L>P	A:82	(19.04, 32.38, 23.05)
9:133333860		Y>H	A:83	(13.32, 30.10, 26.11)
9:133333869	rs121908644	R>C	A:86	(16.35, 26.40, 19.81)
9:133333873		Y>F	A:87	(12.33, 32.54, 21.07)
9:133333884		T>P	A:91	(6.36, 37.65, 20.47)
9:133333888		S>F	A:92	(8.38, 37.96, 24.14)
9:133333905		I>V	A:98	(1.49, 45.87, 23.26)
9:133333908	rs150466363	A>T	A:99	(0.53, 46.33, 27.62)
9:133333911	rs370695114	R>C	A:100	(4.51, 50.39, 27.99)
9:133333912	rs138279074	R>H	A:100	(4.51, 50.39, 27.99)
9:133333929		A>T	A:106	(-7.07, 52.92, 30.22)
9:133333930		A>G	A:106	(-7.07, 52.92, 30.22)
9:133333933	rs149602848	Q>R	A:107	(-4.82, 54.54, 33.56)
9:133333935	rs143405567	R>W	A:108	(-5.30, 58.43, 28.20)
9:133333938	rs371907747	E>K	A:109	(-10.25, 57.04, 28.13)
9:133333951	rs146176455	Y>C	A:113	(-13.31, 46.51, 32.79)
9:133333953		V>M	A:114	(-8.18, 45.43, 29.89)
9:133333962	COSM3929851 CM031623	G>S	A:117	(-7.15, 37.15, 22.17)
9:133333965	COSM1624631 CM940125	A>T	A:118	(-5.35, 35.20, 23.86)
9:133339513	COSM3926289 CM091430	R>W	A:127	(3.97, 37.06, 27.41)
9:133339514	rs201623252 CM034719	R>Q	A:127	(3.97, 37.06, 27.41)
9:133339540		A>S	A:136	(-2.33, 48.36, 37.08)
9:133339541		A>V	A:136	(-2.33, 48.36, 37.08)
9:133342121		P>S	A:144	(-12.64, 35.89, 26.26)
9:133342133	rs369389991	P>S	A:148	(-17.00, 29.74, 30.19)
9:133342143		Y>S	A:151	(-14.36, 28.15, 27.02)
9:133342154		K>E	A:155	(-15.42, 24.95, 19.71)
9:133342160		R>C	A:157	(-12.78, 28.27, 14.13)
9:133342161	rs121908637	R>H	A:157	(-12.78, 28.27, 14.13)
9:133342164		N>S	A:158	(-15.22, 26.60, 11.69)
9:133342172		M>L	A:161	(-15.74, 31.94, 10.41)
9:133346227		G>R	A:168	(-21.17, 40.87, 9.84)
9:133346252		K>R	A:176	(-6.43, 31.15, 6.82)
9:133346255		N>S	A:177	(-2.60, 30.00, 5.91)
9:133346258		P>L	A:178	(-2.91, 25.89, 7.56)
9:133346260	rs121908646	W>R	A:179	(0.14, 28.67, 8.53)
9:133346264	rs121908638	S>N	A:180	(-0.96, 30.87, 13.43)
9:133346272		E>K	A:183	(3.97, 40.34, 11.69)
9:133346279		L>H	A:185	(10.01, 45.31, 13.71)
9:133346287		I>V	A:188	(7.19, 35.94, 11.43)
9:133346873		Y>H	A:190	(5.13, 31.31, 10.79)
9:133346876	COSM1193644 CM031625 CM091432	E>K	A:191	(2.60, 28.26, 16.74)
9:133346898		P>L	A:198	(6.42, 17.69, 15.33)
9:133352260		N>K	A:200	(4.86, 17.52, 9.70)
9:133352261	rs563922134	Q>E	A:201	(8.95, 18.92, 6.81)
9:133352265	rs376371866 CM034721	A>V	A:202	(7.64, 23.48, 6.36)
9:133352267	rs147858743	P>T	A:203	(5.37, 24.34, 3.95)
9:133352273	COSM1701819	G>S	A:205	(5.08, 29.04, 1.57)
9:133352282	rs62637575	T>A	A:208	(6.82, 35.38, 4.34)
9:133352283		T>R	A:208	(6.82, 35.38, 4.34)
9:133352316		T>N	A:219	(27.06, 38.48, -3.97)
9:133352330	COSM3904779	E>K	A:224	(31.15, 48.38, 9.52)
9:133352336	COSM3654882	E>K	A:226	(29.37, 51.42, 15.47)
9:133352337		E>V	A:226	(29.37, 51.42, 15.47)
9:133355120		T>A	A:236	(28.01, 50.71, 6.95)
9:133355124	rs565520844	N>S	A:237	(27.08, 48.36, 2.71)
9:133355126	rs368414392	V>I	A:238	(31.54, 47.95, 2.73)
9:133355160		E>G	A:249	(17.24, 53.83, 9.46)
9:133355162		L>F	A:250	(19.83, 50.29, 12.09)
9:133355169		M>T	A:252	(13.83, 48.54, 9.04)
9:133355180	rs74923032	E>K	A:256	(16.37, 45.32, 3.73)
9:133355186	COSM3904782	A>T	A:258	(18.64, 39.28, 6.12)
9:133355187		A>V	A:258	(18.64, 39.28, 6.12)
9:133355774	rs567807132	G>V	A:259	(16.01, 38.51, 3.96)
9:133355780		H>R	A:261	(21.22, 37.39, 1.74)
9:133355785	rs192838388	V>M	A:263	(19.07, 35.28, 7.54)
9:133355791	rs148918985	R>C	A:265	(14.52, 30.32, 7.36)
9:133355794	rs377221825	I>V	A:266	(14.19, 28.85, 13.76)
9:133355803	rs370595480 CM031627	V>M	A:269	(10.10, 22.24, 20.36)
9:133355806		E>Q	A:270	(8.54, 26.43, 22.57)
9:133355812	COSM1736635 CM940127	R>C	A:272	(3.39, 26.97, 25.58)
9:133355813		R>L	A:272	(3.39, 26.97, 25.58)
9:133355834	rs371265106 COSM455473 CM970121	R>Q	A:279	(6.56, 22.84, 15.45)
9:133355836		G>S	A:280	(7.97, 26.51, 16.03)
9:133364728		E>K	A:283	(11.04, 34.34, 9.66)
9:133364768		D>V	A:296	(32.46, 39.33, 18.24)
9:133364770		I>V	A:297	(31.82, 43.55, 20.34)
9:133364774	rs372061654	E>G	A:298	(30.05, 40.86, 24.66)
9:133364775	rs201419685	E>D	A:298	(30.05, 40.86, 24.66)
9:133364791	rs121908642	R>W	A:304	(37.89, 35.10, 32.04)
9:133364792		R>Q	A:304	(37.89, 35.10, 32.04)
9:133364800	rs183276875	R>C	A:307	(30.92, 36.44, 28.84)
9:133364801	rs571576756 COSM3413382	R>H	A:307	(30.92, 36.44, 28.84)
9:133364805	rs151056441	K>N	A:308	(31.68, 33.70, 33.49)
9:133364809	rs121908648	K>Q	A:310	(26.28, 39.09, 31.26)
9:133364810	rs199751308 CM091438	K>R	A:310	(26.28, 39.09, 31.26)
9:133364816		G>V	A:312	(23.34, 34.54, 33.75)
9:133364846	rs373473841 COSM1319649	Y>C	A:322	(8.80, 32.34, 26.92)
9:133364851	rs121908639	G>S	A:324	(6.09, 37.83, 31.58)
9:133370280		F>V	A:333	(18.75, 43.49, 39.87)
9:133370286	rs373514077 COSM1238243	R>C	A:335	(15.89, 45.26, 32.65)
9:133370287	rs555388438	R>H	A:335	(15.89, 45.26, 32.65)
9:133370298	rs145100866	A>T	A:339	(23.52, 47.66, 31.45)
9:133370334		V>M	A:351	(29.43, 41.12, 9.04)
9:133370340	COSM3765430	V>I	A:353	(24.97, 38.47, 4.76)
9:133370355		V>M	A:358	(25.78, 35.42, 9.66)
9:133370367		G>S	A:362	(35.89, 41.23, 12.18)
9:133370371	COSM462438 CM940129 CM031630	R>Q	A:363	(36.86, 41.29, 15.44)
9:133374899	rs78549067	V>M	A:379	(57.45, 37.88, 20.53)
9:133374904		Q>H	A:380	(57.74, 37.53, 23.74)
9:133374909		D>V	A:382	(54.51, 41.33, 29.24)
9:133374917		P>A	A:385	(57.41, 31.60, 30.35)
9:133374920	rs376164698	T>P	A:386	(58.54, 30.36, 34.48)
9:133374929	rs145288815	T>A	A:389	(55.27, 26.20, 35.33)
9:133374933		G>E	A:390	(53.06, 27.17, 38.49)
9:133374943		N>K	A:393	(52.62, 22.70, 38.93)
9:133376379		R>C	A:404	(47.46, 10.39, 47.76)
9:133376380		R>H	A:404	(47.46, 10.39, 47.76)

2NZ2.A | ASS1.

2NZ2.A | ASS1

General Structure Information

Variant Set Distributions

Ripley’s K Analysis Plots

Variant Set Comparisons

Pathogenic Proximity Analysis

Mapped Variants

[+] ExAC Missense Variants

[+] ClinVar Missense Variants

[+] COSMIC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
9:133333965	COSM1624631	A>T	A:118	(-5.35, 35.20, 23.86)
9:133355773	COSM1701820	G>S	A:259	(16.01, 38.51, 3.96)
9:133364801	COSM3413382	R>H	A:307	(30.92, 36.44, 28.84)