2V9K.A | PUS10

General Structure Information

PDB ID	2v9k
HGNC Gene Label(s)	PUS10
Structure Name	crystal structure of human pus10, a novel pseudouridine synthase.
Resolution	2.0Å
Reference	AUTH C.J.MCCLEVERTY,M.HORNSBY,G.SPRAGGON,A.KREUSCHTITL CRYSTAL STRUCTURE OF HUMAN PUS10, A NOVEL PSEUDOURIDINETITL 2 SYNTHASE.REF J.MOL.BIOL. V. 373 1243 2007REFN ISSN 0022-2836PMID 17900615DOI 10.1016/J.JMB.2007.08.053

Variant Set Distributions

ExAC Variants

Number Of Residues	466
Number Of SNVs	135
Number Of Permutations	46178
Optimal Distance Threshold	35.0
K Statistic	0.438
p-value	0.553

COSMIC

Number Of Residues	466
Number Of SNVs	3
Number Of Permutations	459
Optimal Distance Threshold	11.0
K Statistic	0.333
p-value	0.615

Ripley’s K Analysis Plots

ExACCOSMIC

Variant Set Comparisons

Cosmic vs. ExAC

Number Of ExAC SNVs	135
Number Of COSMIC SNVs	3
Optimal Distance Threshold	11.0
K Statistic	0.285
p-value	0.861

Pathogenic Proximity Analysis

COSMIC PathProx Analysis

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
2:61239018	rs139165346	P>L	A:3	(-29.64, 2.12, -29.11)
2:61239010		E>Q	A:6	(-28.16, 12.26, -35.13)
2:61238996		H>Q	A:10	(-21.36, 14.91, -32.32)
2:61238991		A>V	A:12	(-19.96, 8.56, -29.79)
2:61238986		L>V	A:14	(-15.10, 12.15, -28.98)
2:61238982		L>S	A:15	(-16.09, 8.50, -26.40)
2:61238979	rs531613624	L>H	A:16	(-14.91, 5.23, -30.72)
2:61238980	COSM1408818	L>F	A:16	(-14.91, 5.23, -30.72)
2:61238976		N>S	A:17	(-12.19, 8.56, -32.03)
2:61238973	rs147445494	T>I	A:18	(-10.56, 8.66, -27.54)
2:61238967		T>S	A:20	(-14.35, 4.41, -25.31)
2:61238964	rs372163151	C>Y	A:21	(-16.23, 0.77, -25.06)
2:61238953		I>F	A:25	(-20.30, 4.77, -25.81)
2:61238940	rs552338244	C>Y	A:29	(-25.55, 7.98, -24.12)
2:61238935	rs527451210	V>M	A:31	(-28.52, 3.40, -22.61)
2:61238932		D>Y	A:32	(-31.47, 3.16, -19.06)
2:61238925	rs560194306	H>R	A:34	(-31.10, -3.86, -19.07)
2:61238916		Y>C	A:37	(-25.62, -2.28, -22.27)
2:61238910	rs200105134	L>P	A:39	(-25.55, -7.51, -28.15)
2:61238902		K>E	A:42	(-18.69, -7.64, -32.54)
2:61236140	rs578029887	N>S	A:46	(-19.55, -4.02, -36.39)
2:61236120		E>K	A:53	(-20.72, 4.97, -41.38)
2:61235951		C>Y	A:109	(-11.43, 0.75, -22.31)
2:61235946		V>I	A:111	(-13.34, 4.20, -19.13)
2:61235932		I>M	A:115	(-14.90, -4.42, -16.60)
2:61235928		Q>E	A:117	(-14.17, -5.05, -23.02)
2:61235912		K>R	A:122	(-20.82, -17.30, -21.47)
2:61233775		C>R	A:129	(-19.21, -20.34, -11.88)
2:61233756		S>Y	A:135	(-16.31, -24.26, -2.95)
2:61233757		S>T	A:135	(-16.31, -24.26, -2.95)
2:61233738		S>T	A:141	(-29.53, -18.04, -4.16)
2:61233739	rs375158501	S>G	A:141	(-29.53, -18.04, -4.16)
2:61233707	rs201699663	Q>H	A:151	(-7.75, 3.27, -10.15)
2:61233700	rs553997820	V>I	A:154	(-10.11, 9.15, -12.11)
2:61198666		Q>H	A:165	(-15.95, 19.96, -23.47)
2:61198667		Q>P	A:165	(-15.95, 19.96, -23.47)
2:61194720		D>Y	A:178	(-27.72, 11.52, -16.88)
2:61194686		I>T	A:189	(-24.35, -7.86, -18.76)
2:61194687		I>L	A:189	(-24.35, -7.86, -18.76)
2:61194666	rs576123297	E>K	A:196	(-27.99, -20.18, -17.85)
2:61194656		G>D	A:199	(-29.36, -22.36, -11.46)
2:61194651		P>T	A:201	(-32.02, -17.33, -8.40)
2:61194642	rs566792214	G>R	A:204	(-30.22, -9.60, -2.60)
2:61194638		K>R	A:205	(-32.77, -10.04, 0.70)
2:61192612		F>C	A:208	(-23.86, -17.99, -1.92)
2:61192602		S>R	A:211	(-16.87, -12.09, -4.72)
2:61192598		V>F	A:213	(-11.76, -8.21, -6.68)
2:61192585		P>L	A:217	(-1.52, -2.70, -11.12)
2:61192583		E>K	A:218	(-0.78, 0.24, -15.43)
2:61192579	rs376959009	T>R	A:219	(-3.42, 2.72, -12.75)
2:61192567		C>F	A:223	(-5.01, 6.90, -5.59)
2:61192561		F>C	A:225	(-0.95, 11.00, -8.55)
2:61192233	COSM4095018	A>V	A:228	(-1.88, 15.64, -3.54)
2:61192227	rs550921656	C>Y	A:230	(-7.54, 16.42, -1.27)
2:61192228	rs150107494	C>R	A:230	(-7.54, 16.42, -1.27)
2:61192221		D>G	A:232	(-8.86, 15.29, 4.01)
2:61190016		T>S	A:245	(-12.13, 3.68, -0.85)
2:61190006		A>E	A:248	(-12.71, 8.28, -1.03)
2:61189999	rs186159457	M>I	A:250	(-16.18, 8.97, -5.65)
2:61189995		A>T	A:252	(-12.35, 13.72, -3.88)
2:61189989		N>H	A:254	(-17.60, 15.69, -5.51)
2:61189974	rs552965970	E>K	A:259	(-8.23, 23.13, -12.82)
2:61188669		P>L	A:268	(-8.86, 12.03, -22.92)
2:61188670		P>S	A:268	(-8.86, 12.03, -22.92)
2:61188663		N>S	A:270	(-4.80, 7.81, -21.79)
2:61188658		P>S	A:272	(-4.55, 0.94, -21.22)
2:61188652		A>P	A:274	(-3.84, -3.81, -19.86)
2:61188646		C>R	A:276	(-8.21, -5.56, -15.29)
2:61188643	rs113622721	A>T	A:277	(-6.75, -7.99, -12.78)
2:61188640		V>I	A:278	(-8.86, -11.17, -11.45)
2:61188633	rs188957240	E>A	A:280	(-10.11, -11.50, -4.74)
2:61188624		C>Y	A:283	(-17.50, -17.89, -2.03)
2:61188616		G>S	A:286	(-24.14, -17.01, 5.79)
2:61187634		S>C	A:298	(-23.00, -29.41, 36.70)
2:61187628	rs372174292	N>S	A:300	(-17.61, -28.12, 38.22)
2:61187622		P>R	A:302	(-18.52, -23.30, 32.89)
2:61187616	rs377112557	T>N	A:304	(-18.51, -19.78, 28.82)
2:61187580	COSM176923	S>C	A:316	(-15.67, -27.48, 29.37)
2:61187569		E>K	A:320	(-17.15, -26.22, 24.76)
2:61187551		L>V	A:326	(-22.84, -28.17, 15.56)
2:61187542		V>I	A:329	(-22.88, -31.02, 10.89)
2:61187528		E>D	A:333	(-15.14, -21.02, 9.53)
2:61182195		S>P	A:339	(-27.74, -16.85, 26.03)
2:61182179		D>G	A:344	(-23.16, -18.81, 38.50)
2:61182177		V>I	A:345	(-20.15, -22.56, 37.98)
2:61182173	rs146710040	D>V	A:346	(-22.58, -23.14, 41.71)
2:61182158		G>A	A:351	(-36.63, -27.81, 33.41)
2:61181278	rs551654092	I>T	A:358	(-25.23, -21.83, 18.01)
2:61181279	rs563556086	I>V	A:358	(-25.23, -21.83, 18.01)
2:61181270		V>L	A:361	(-19.39, -18.94, 10.50)
2:61181260		H>R	A:364	(-19.39, -24.95, 3.36)
2:61181252	rs141963314	H>Y	A:367	(-30.01, -27.42, 2.76)
2:61181243		S>A	A:370	(-36.82, -31.72, 11.35)
2:61181239	rs112614800	Q>R	A:371	(-35.62, -36.47, 12.03)
2:61181120	rs377425600	I>V	A:380	(-25.83, -33.02, 21.90)
2:61181107		S>F	A:384	(-23.39, -35.28, 28.33)
2:61181092		V>A	A:389	(-30.47, -29.99, 24.35)
2:61181089		R>H	A:390	(-35.38, -29.25, 25.98)
2:61181090	rs144588759	R>C	A:390	(-35.38, -29.25, 25.98)
2:61181079		Q>H	A:393	(-35.43, -24.91, 16.50)
2:61180232	COSM1738809	M>T	A:403	(-31.98, -14.54, 23.47)
2:61180209		T>A	A:411	(-39.56, -13.79, 34.95)
2:61180189		L>F	A:417	(-30.54, -25.39, 50.34)
2:61180178	COSM1663776	N>S	A:421	(-27.47, -19.11, 62.68)
2:61180169		I>T	A:424	(-35.46, -22.93, 62.06)
2:61180157		D>V	A:428	(-39.91, -19.77, 62.18)
2:61180154		I>T	A:429	(-40.33, -20.51, 57.14)
2:61180143		N>D	A:433	(-45.36, -18.48, 52.05)
2:61180136		I>T	A:435	(-44.02, -11.94, 51.18)
2:61175311		I>V	A:440	(-35.12, -5.87, 46.73)
2:61175299		T>A	A:444	(-23.34, -4.18, 42.71)
2:61175296		P>S	A:445	(-22.89, -7.73, 43.73)
2:61175290	rs368473144	R>G	A:447	(-20.63, -12.29, 43.11)
2:61175287		V>I	A:448	(-19.78, -8.53, 40.37)
2:61175284		L>V	A:449	(-17.81, -4.55, 42.38)
2:61175280		H>R	A:450	(-14.67, -7.64, 39.02)
2:61175271		P>R	A:453	(-20.86, -0.56, 37.50)
2:61175268		L>P	A:454	(-21.45, 0.96, 42.51)
2:61175265	rs375056493	A>D	A:455	(-25.38, 0.29, 41.56)
2:61175259	rs141037128	R>Q	A:457	(-30.40, -3.47, 39.83)
2:61175251	rs377687971	V>L	A:460	(-39.44, -7.60, 42.42)
2:61175244		H>R	A:462	(-42.66, -11.32, 41.61)
2:61175245	rs201669454	H>Y	A:462	(-42.66, -11.32, 41.61)
2:61175221	rs373270609 COSM3723279	D>Y	A:470	(-33.40, -29.09, 59.19)
2:61175208		F>C	A:474	(-35.24, -22.66, 54.44)
2:61175206	COSM1022026	R>C	A:475	(-35.17, -26.94, 49.94)
2:61175202	rs547221084	L>P	A:476	(-36.83, -20.44, 48.94)
2:61175193	COSM1327022	K>I	A:479	(-41.47, -15.35, 40.15)
2:61175191		T>S	A:480	(-37.30, -13.10, 40.31)
2:61175187	rs201759127	Q>R	A:481	(-37.22, -8.25, 38.26)
2:61175184		A>G	A:482	(-34.82, -9.57, 35.76)
2:61175185	rs369402051	A>P	A:482	(-34.82, -9.57, 35.76)
2:61172239		I>V	A:486	(-30.95, -15.07, 44.17)
2:61172233		E>Q	A:488	(-26.40, -11.69, 46.93)
2:61172223	rs373867073 COSM1185918	H>R	A:491	(-25.88, -13.57, 51.55)
2:61172224	rs186143186	H>Y	A:491	(-25.88, -13.57, 51.55)
2:61172213	rs151124462	F>L	A:494	(-21.53, -8.46, 54.34)
2:61172212		G>R	A:495	(-26.38, -5.13, 53.57)
2:61172193		I>T	A:501	(-33.96, -14.28, 53.84)
2:61172191	rs369875737 COSM443068	G>R	A:502	(-32.11, -12.60, 57.38)
2:61172187		S>C	A:503	(-33.55, -9.43, 57.66)
2:61172175		V>G	A:507	(-31.31, -15.26, 60.81)
2:61172163		I>N	A:511	(-27.12, -20.00, 49.34)
2:61172155		L>M	A:514	(-29.03, -21.81, 43.18)
2:61172144		E>D	A:517	(-36.50, -24.48, 38.71)
2:61169559		V>F	A:521	(-38.18, -16.94, 27.61)
2:61169538	rs367798034	D>N	A:528	(-44.25, -31.65, 20.05)

2V9K.A | PUS10.

2V9K.A | PUS10

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
2:61192559	COSM3054082	L>I	A:226	(-6.63, 12.43, -5.67)
2:61180187	COSM3734430	I>S	A:418	(-31.64, -21.62, 52.84)
2:61180178	COSM1663776	N>S	A:421	(-27.47, -19.11, 62.68)