3U1K.D | PNPT1

General Structure Information

PDB ID	3u1k
HGNC Gene Label(s)	PNPT1
Structure Name	crystal structure of human pnpase
Resolution	2.13Å
Reference	AUTH C.L.LIN,Y.-T.WANG,W.-Z.YANG,Y.-Y.HSIAO,H.S.YUANTITL CRYSTAL STRUCTURE OF HUMAN POLYNUCLEOTIDE PHOSPHORYLASE:TITL 2 INSIGHTS INTO ITS DOMAIN FUNCTION IN RNA BINDING ANDTITL 3 DEGRADATIONREF NUCLEIC ACIDS RES. V. 40 4146 2012REFN ISSN 0305-1048PMID 22210891DOI 10.1093/NAR/GKR1281

Variant Set Distributions

ExAC Variants

Number Of Residues	611
Number Of SNVs	151
Number Of Permutations	77315
Optimal Distance Threshold	11.0
K Statistic	0.045
p-value	0.657

ClinVar

Number Of Residues	611
Number Of SNVs	10
Number Of Permutations	8774
Optimal Distance Threshold	16.0
K Statistic	0.378
p-value	0.003

COSMIC

Number Of Residues	611
Number Of SNVs	5
Number Of Permutations	791
Optimal Distance Threshold	14.0
K Statistic	0.2
p-value	0.416

Ripley’s K Analysis Plots

ExACClinVarCOSMIC

Variant Set Comparisons

ClinVar vs. ExAC

Number Of ExAC SNVs	151
Number Of ClinVar SNVs	10
Optimal Distance Threshold	16.0
K Statistic	0.267
p-value	0.006

Cosmic vs. ExAC

Number Of ExAC SNVs	151
Number Of COSMIC SNVs	5
Optimal Distance Threshold	43.0
K Statistic	0.283
p-value	0.715

Pathogenic Proximity Analysis

ClinVar PathProx Analysis

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
2:55920822	rs540498342	A>G	D:46	(-82.89, -70.36, 37.49)
2:55920810		D>V	D:50	(-89.50, -78.12, 28.38)
2:55914828		I>M	D:58	(-84.05, -68.34, 31.84)
2:55914821		G>R	D:61	(-77.05, -63.06, 39.32)
2:55914816		K>N	D:62	(-73.50, -65.15, 37.59)
2:55914788		V>I	D:72	(-78.58, -65.54, 30.88)
2:55913570		T>A	D:78	(-76.11, -70.36, 22.30)
2:55913566		A>G	D:79	(-75.19, -67.64, 25.24)
2:55913551	rs145552327	A>V	D:84	(-81.64, -53.08, 31.44)
2:55913528		P>S	D:92	(-85.63, -34.21, 27.38)
2:55913506		V>G	D:99	(-82.19, -47.99, 22.54)
2:55912143		P>L	D:113	(-63.49, -62.86, 14.20)
2:55912097		I>M	D:128	(-79.64, -53.07, 12.49)
2:55912098		I>T	D:128	(-79.64, -53.07, 12.49)
2:55912096	rs147272640	L>V	D:129	(-82.71, -56.32, 11.18)
2:55912084		I>V	D:133	(-87.08, -57.87, 15.94)
2:55912081		I>V	D:134	(-85.53, -56.86, 20.34)
2:55910967		R>C	D:136	(-90.79, -54.37, 16.15)
2:55910961	rs76401964	I>V	D:138	(-89.80, -54.52, 24.30)
2:55910954	rs572684828	P>L	D:140	(-95.46, -52.35, 23.23)
2:55910955		P>S	D:140	(-95.46, -52.35, 23.23)
2:55910943		A>T	D:144	(-97.89, -44.42, 29.44)
2:55910930	rs202197669	Y>C	D:148	(-88.44, -41.79, 32.53)
2:55910925	rs142364070	T>A	D:150	(-84.42, -46.99, 28.20)
2:55908049	rs368986484	L>R	D:153	(-77.17, -53.66, 25.62)
2:55908043		N>S	D:155	(-73.10, -60.02, 25.31)
2:55908040	rs554911413	L>Q	D:156	(-73.42, -62.76, 21.78)
2:55908041		L>V	D:156	(-73.42, -62.76, 21.78)
2:55908037	rs374683384	L>S	D:157	(-71.69, -64.76, 26.36)
2:55908034		A>V	D:158	(-71.80, -67.93, 23.21)
2:55908035		A>S	D:158	(-71.80, -67.93, 23.21)
2:55908031		V>A	D:159	(-72.18, -68.70, 19.35)
2:55908025	rs150329481	G>V	D:161	(-73.85, -72.48, 15.14)
2:55908019		N>S	D:163	(-78.66, -73.03, 18.76)
2:55908014	rs151166046	P>S	D:165	(-78.57, -65.85, 18.69)
2:55907990		A>T	D:173	(-85.25, -58.47, 27.19)
2:55907885	rs566212594	A>V	D:176	(-84.33, -58.13, 32.04)
2:55907865		P>S	D:183	(-91.73, -49.85, 34.65)
2:55906921	COSM3426561	R>Q	D:192	(-87.13, -68.38, 14.54)
2:55906913		I>V	D:195	(-92.39, -74.95, 7.51)
2:55906901		E>K	D:199	(-93.10, -81.44, 9.99)
2:55906894		V>A	D:201	(-90.16, -76.46, 13.50)
2:55906880		R>G	D:206	(-76.79, -72.80, 10.54)
2:55906864		S>F	D:211	(-84.68, -76.40, 4.92)
2:55906859		T>S	D:213	(-91.00, -72.69, 3.88)
2:55906850		L>V	D:216	(-92.50, -66.76, 12.00)
2:55906847		V>M	D:217	(-90.52, -64.24, 14.78)
2:55906828		K>R	D:223	(-104.23, -63.21, 28.33)
2:55906829		K>E	D:223	(-104.23, -63.21, 28.33)
2:55900206	rs34928857	E>Q	D:230	(-90.88, -60.19, 11.29)
2:55900190		N>T	D:235	(-95.23, -68.06, -2.07)
2:55900160		I>T	D:245	(-99.11, -67.42, 13.77)
2:55900154		V>A	D:247	(-97.57, -72.97, 16.85)
2:55900149		V>M	D:249	(-98.71, -68.02, 20.36)
2:55900142		Y>C	D:251	(-94.20, -73.74, 21.49)
2:55900143		Y>N	D:251	(-94.20, -73.74, 21.49)
2:55900089		T>A	D:269	(-89.48, -54.37, 43.59)
2:55900080		T>S	D:272	(-91.99, -45.26, 42.02)
2:55900065		F>L	D:277	(-94.84, -37.28, 31.78)
2:55900061	rs572632492	T>S	D:278	(-100.49, -38.77, 31.58)
2:55900050		E>K	D:282	(-108.76, -32.51, 34.71)
2:55900034		T>I	D:287	(-109.46, -30.26, 25.32)
2:55900032	rs141543222	H>Y	D:288	(-113.84, -33.40, 24.12)
2:55899179		L>H	D:290	(-112.49, -26.13, 23.47)
2:55899174	rs533576539 COSM1581495	M>V	D:292	(-115.73, -32.35, 19.32)
2:55899165		L>V	D:295	(-111.41, -32.07, 15.57)
2:55899161	rs137893343	Y>C	D:296	(-117.26, -34.93, 13.40)
2:55899156	rs534505993	V>L	D:298	(-111.54, -31.96, 9.93)
2:55899140		E>V	D:303	(-112.55, -32.29, -0.39)
2:55899141	rs201351041	E>K	D:303	(-112.55, -32.29, -0.39)
2:55898511		V>F	D:307	(-101.14, -31.04, 3.97)
2:55898497		E>D	D:311	(-102.40, -27.23, 7.46)
2:55898486	rs35405862	K>R	D:315	(-106.23, -23.55, 12.44)
2:55898471	rs200555807 COSM1408714	T>M	D:320	(-107.25, -25.25, 21.91)
2:55898467		E>D	D:321	(-102.72, -25.36, 22.73)
2:55898468		E>A	D:321	(-102.72, -25.36, 22.73)
2:55895075		D>G	D:332	(-96.51, -28.23, 31.22)
2:55895076		D>N	D:332	(-96.51, -28.23, 31.22)
2:55895073	rs538713029	P>S	D:333	(-96.66, -26.50, 28.25)
2:55895069	COSM1614975	Y>C	D:334	(-94.10, -29.69, 27.48)
2:55895058		E>K	D:338	(-99.98, -35.32, 25.34)
2:55895048		N>S	D:341	(-102.29, -34.94, 20.86)
2:55895043		V>L	D:343	(-108.71, -35.05, 22.04)
2:55895028		F>V	D:348	(-109.25, -40.36, 13.50)
2:55895021	rs570650958	S>I	D:350	(-114.98, -42.07, 17.04)
2:55895010		N>Y	D:354	(-119.36, -44.80, 15.99)
2:55895000		K>R	D:357	(-117.11, -43.42, 6.70)
2:55895001		K>Q	D:357	(-117.11, -43.42, 6.70)
2:55894224		D>N	D:360	(-110.73, -40.66, 3.11)
2:55894221		G>S	D:361	(-114.38, -41.85, 3.04)
2:55894217	rs369037911	R>Q	D:362	(-110.70, -45.07, 2.55)
2:55894218	rs151216278	R>W	D:362	(-110.70, -45.07, 2.55)
2:55894203	rs142840568	L>F	D:367	(-107.56, -49.84, -2.09)
2:55894190	rs538251642	S>N	D:371	(-101.06, -45.55, -10.14)
2:55894181	rs377657203	V>A	D:374	(-93.21, -49.16, -16.68)
2:55894179		D>H	D:375	(-90.13, -47.93, -19.91)
2:55894175	rs143647681	M>T	D:376	(-89.97, -44.26, -16.77)
2:55894154	COSM1483167	S>L	D:383	(-88.40, -48.65, -14.40)
2:55894155		S>A	D:383	(-88.40, -48.65, -14.40)
2:55894130		T>I	D:391	(-97.54, -42.96, -1.48)
2:55894127	COSM575638	Q>R	D:392	(-94.35, -41.04, -5.42)
2:55889149	rs200016391	V>I	D:397	(-83.59, -52.54, -12.14)
2:55889107	rs551750608	V>I	D:411	(-63.59, -60.13, 7.35)
2:55887326		G>E	D:417	(-72.47, -61.74, 2.98)
2:55887324		I>V	D:418	(-72.84, -63.79, -0.46)
2:55887304		M>I	D:424	(-79.49, -56.34, -3.33)
2:55887298		H>Q	D:426	(-80.98, -49.26, -1.30)
2:55883490		T>N	D:434	(-92.15, -35.34, 4.35)
2:55883491		T>S	D:434	(-92.15, -35.34, 4.35)
2:55883478		G>V	D:438	(-82.13, -34.01, 6.31)
2:55883448	COSM1021903	L>P	D:448	(-81.74, -51.55, 6.56)
2:55883449		L>I	D:448	(-81.74, -51.55, 6.56)
2:55883352	rs376803449	A>V	D:452	(-85.35, -55.93, 4.15)
2:55883350	rs141173235	L>F	D:453	(-89.85, -55.89, 4.37)
2:55883325		V>A	D:461	(-90.35, -64.31, -7.20)
2:55883316		R>Q	D:464	(-81.59, -69.97, -7.43)
2:55883311	rs557649588 COSM1021902	F>L	D:466	(-80.23, -63.61, -13.73)
2:55883275	rs146990953	E>Q	D:478	(-94.80, -38.53, -3.02)
2:55882076	rs138669964	M>T	D:485	(-95.45, -52.75, 1.08)
2:55882077		M>L	D:485	(-95.45, -52.75, 1.08)
2:55882074		A>S	D:486	(-94.71, -49.72, -2.62)
2:55882068		A>T	D:488	(-92.64, -54.31, -3.54)
2:55882062		G>S	D:490	(-92.32, -51.70, -7.94)
2:55882059		G>R	D:491	(-90.32, -54.05, -8.00)
2:55882055		S>N	D:492	(-92.60, -56.39, -9.38)
2:55874586		V>F	D:500	(-86.27, -60.60, -14.46)
2:55874580		I>V	D:502	(-90.45, -62.72, -11.82)
2:55874573		S>F	D:504	(-95.11, -64.10, -9.70)
2:55874568		V>I	D:506	(-95.23, -59.13, -5.62)
2:55874565	rs143712760	A>S	D:507	(-97.95, -57.17, -3.50)
2:55874558		V>A	D:509	(-100.91, -53.98, 2.15)
2:55874559	rs146571352	V>I	D:509	(-100.91, -53.98, 2.15)
2:55874501	rs367713105 COSM4094926	R>H	D:528	(-114.02, -51.02, 13.63)
2:55874502		R>C	D:528	(-114.02, -51.02, 13.63)
2:55874492	rs374698153	T>R	D:531	(-107.39, -51.50, 3.88)
2:55873621		G>R	D:535	(-100.70, -42.02, 8.48)
2:55873605	rs202190573	N>S	D:540	(-104.34, -41.75, 15.42)
2:55873567		G>R	D:553	(-99.09, -66.06, -1.34)
2:55873456	rs149843729	A>G	D:559	(-96.24, -56.57, 12.75)
2:55873432		P>R	D:567	(-106.17, -60.64, 19.75)
2:55873430		I>V	D:568	(-104.83, -64.93, 17.56)
2:55873426		K>R	D:569	(-110.28, -62.70, 15.98)
2:55873418	rs75290562	M>V	D:572	(-105.80, -64.62, 11.59)
2:55873414	rs373628268 COSM1408713	E>A	D:573	(-109.86, -61.11, 10.94)
2:55873412		A>T	D:574	(-105.66, -59.14, 8.75)
2:55872561		K>R	D:582	(-102.50, -59.29, -2.29)
2:55872551		I>M	D:585	(-102.80, -54.09, -5.59)
2:55872552		I>T	D:585	(-102.80, -54.09, -5.59)
2:55872548		L>F	D:586	(-101.67, -58.03, -8.00)
2:55872544		I>F	D:588	(-104.29, -52.37, -10.73)
2:55872540		M>T	D:589	(-99.64, -54.34, -10.70)
2:55872537		N>S	D:590	(-101.12, -57.33, -14.43)
2:55872538	rs7594497	N>D	D:590	(-101.12, -57.33, -14.43)
2:55872534		K>T	D:591	(-104.41, -52.88, -16.01)
2:55872535	rs542676905	K>Q	D:591	(-104.41, -52.88, -16.01)
2:55872525		S>L	D:594	(-98.33, -59.25, -17.13)
2:55872526	rs200944866	S>A	D:594	(-98.33, -59.25, -17.13)
2:55872521	rs368876074	K>N	D:595	(-95.57, -60.61, -19.72)
2:55872516		R>Q	D:597	(-89.04, -56.22, -21.57)
2:55872511	rs147375807	S>T	D:599	(-85.62, -59.42, -23.42)
2:55871844		V>F	D:612	(-55.09, -64.64, -23.71)
2:55871828		R>Q	D:617	(-51.21, -63.86, -18.03)
2:55871825		A>E	D:618	(-48.19, -60.45, -18.86)
2:55871822		K>R	D:619	(-48.36, -56.91, -22.66)
2:55871823		K>E	D:619	(-48.36, -56.91, -22.66)
2:55870552		I>V	D:639	(-61.80, -58.82, -16.34)
2:55870536		E>A	D:644	(-53.71, -71.42, -18.93)
2:55870530	COSM4094923	T>M	D:646	(-60.01, -68.22, -20.57)
2:55870507		P>S	D:654	(-73.07, -52.88, -25.35)
2:55870498		M>V	D:657	(-67.43, -55.28, -24.45)
2:55870494	rs545932442	H>R	D:658	(-66.05, -51.10, -28.49)
2:55870489		A>S	D:660	(-62.36, -53.82, -23.80)
2:55870485	rs201269381	R>K	D:661	(-63.50, -57.52, -27.20)

3U1K.D | PNPT1.

3U1K.D | PNPT1

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
2:55912093	COSM3053551	T>A	D:130	(-82.02, -58.24, 15.72)
2:55906921	COSM3426561	R>Q	D:192	(-87.13, -68.38, 14.54)
2:55900055	COSM3839738	S>L	D:280	(-105.23, -34.24, 33.19)
2:55895069	COSM1614975	Y>C	D:334	(-94.10, -29.69, 27.48)
2:55883470	COSM1614974	T>A	D:441	(-75.23, -39.40, 5.51)