4FDJ.A | GALNS

General Structure Information

PDB ID	4fdj
HGNC Gene Label(s)	GALNS
Structure Name	the molecular basis of mucopolysaccharidosis iv a, complex with galnac
Resolution	2.81Å
Reference	AUTH Y.RIVERA-COLON,E.K.SCHUTSKY,A.Z.KITA,S.C.GARMANTITL THE STRUCTURE OF HUMAN GALNS REVEALS THE MOLECULAR BASIS FORTITL 2 MUCOPOLYSACCHARIDOSIS IV A.REF J.MOL.BIOL. V. 423 736 2012REFN ISSN 0022-2836PMID 22940367DOI 10.1016/J.JMB.2012.08.020

Variant Set Distributions

ExAC Variants

Number Of Residues	492
Number Of SNVs	156
Number Of Permutations	62481
Optimal Distance Threshold	9.0
K Statistic	0.027
p-value	0.196

ClinVar

Number Of Residues	492
Number Of SNVs	20
Number Of Permutations	12700
Optimal Distance Threshold	11.0
K Statistic	0.116
p-value	0.017

COSMIC

Number Of Residues	492
Number Of SNVs	3
Number Of Permutations	137
Optimal Distance Threshold	9.0
K Statistic	0.333
p-value	0.227

Ripley’s K Analysis Plots

ExACClinVarCOSMIC

Variant Set Comparisons

ClinVar vs. ExAC

Number Of ExAC SNVs	156
Number Of ClinVar SNVs	18
Optimal Distance Threshold	11.0
K Statistic	0.069
p-value	0.021

Cosmic vs. ExAC

Number Of ExAC SNVs	156
Number Of COSMIC SNVs	3
Optimal Distance Threshold	9.0
K Statistic	0.307
p-value	0.519

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
16:88923194		P>L	A:31	(10.50, -6.96, 32.20)
16:88923191		N>S	A:32	(6.39, -5.29, 31.46)
16:88923179		L>R	A:36	(4.79, 2.33, 20.80)
16:88909219	rs199638097 CM970574	G>R	A:47	(9.78, 17.85, 18.16)
16:88909209		G>A	A:50	(12.36, 19.42, 14.63)
16:88909188	rs148197417	P>L	A:57	(4.05, 17.09, 24.10)
16:88909189		P>S	A:57	(4.05, 17.09, 24.10)
16:88909180	rs118204447	D>N	A:60	(9.03, 15.73, 23.42)
16:88909176		R>Q	A:61	(6.74, 14.77, 29.04)
16:88909177	rs145798311	R>W	A:61	(6.74, 14.77, 29.04)
16:88909167		A>V	A:64	(13.44, 13.50, 28.63)
16:88909168	rs527906032	A>T	A:64	(13.44, 13.50, 28.63)
16:88909159	rs11862754	L>M	A:67	(17.66, 6.93, 24.83)
16:88909147		N>D	A:71	(21.49, 7.18, 13.91)
16:88909144		F>V	A:72	(16.51, 3.20, 14.71)
16:88909129	rs201278722	P>A	A:77	(10.65, 0.90, 2.08)
16:88909117		P>S	A:81	(7.99, -5.69, 4.82)
16:88908355		R>Q	A:90	(14.65, -13.28, 9.89)
16:88908320	rs372585484	A>T	A:102	(10.69, -7.58, -10.50)
16:88908316		H>R	A:103	(14.96, -7.33, -10.34)
16:88908305	COSM974792 CM042055	A>T	A:107	(5.77, -5.29, -1.72)
16:88907497	rs200242926	T>A	A:109	(0.03, -7.46, 2.67)
16:88907485	rs118204438	I>F	A:113	(-1.71, -11.44, -0.95)
16:88907482		V>M	A:114	(-1.88, -15.87, -1.52)
16:88907463	rs112454391	S>L	A:120	(8.95, -21.27, 9.58)
16:88907448		P>L	A:125	(4.96, -13.31, 20.43)
16:88907444		E>D	A:126	(5.61, -17.66, 18.91)
16:88907435		K>N	A:129	(4.08, -17.99, 25.18)
16:88907433		K>T	A:130	(9.83, -19.55, 25.90)
16:88907430		A>D	A:131	(8.71, -16.11, 30.01)
16:88907428		G>S	A:132	(5.08, -15.71, 30.70)
16:88907416		K>Q	A:136	(-3.18, -7.23, 22.99)
16:88907412		I>S	A:137	(-2.05, -7.05, 18.23)
16:88907410	rs140018158	V>I	A:138	(-3.42, -2.94, 19.20)
16:88907407	rs146093755	G>S	A:139	(-4.12, -3.02, 15.18)
16:88907403		K>R	A:140	(-1.61, -2.35, 10.79)
16:88904161		H>Q	A:145	(-5.86, -11.81, 4.51)
16:88904163	rs577334837	H>Y	A:145	(-5.86, -11.81, 4.51)
16:88904156		P>L	A:147	(-7.09, -17.97, 7.90)
16:88904144	rs559063128 COSM3513226 CM950532	P>L	A:151	(-2.40, -12.99, 14.83)
16:88904145		P>T	A:151	(-2.40, -12.99, 14.83)
16:88904136		H>Y	A:154	(1.39, -16.70, 13.98)
16:88904133	rs398123438 COSM3672336 CM970584	G>R	A:155	(1.40, -15.69, 19.73)
16:88904111	rs118204444	S>F	A:162	(-6.98, -4.84, 10.78)
16:88904102		C>Y	A:165	(-5.78, -1.05, 5.11)
16:88904094		G>R	A:168	(-12.01, 3.41, 1.20)
16:88904080	rs367557149	N>K	A:172	(-19.00, -4.96, -0.73)
16:88904081	rs149399411	N>S	A:172	(-19.00, -4.96, -0.73)
16:88904082		N>D	A:172	(-19.00, -4.96, -0.73)
16:88904076		A>T	A:174	(-15.01, -5.53, -6.31)
16:88904072		R>K	A:175	(-11.45, -4.47, -3.65)
16:88902665		E>K	A:193	(-19.65, -1.84, 11.78)
16:88902655		I>N	A:196	(-13.50, 6.31, 8.21)
16:88902643	rs7187889	T>M	A:200	(-14.30, 15.36, 8.15)
16:88902640		G>E	A:201	(-11.57, 12.82, 9.31)
16:88902641		G>R	A:201	(-11.57, 12.82, 9.31)
16:88902619	rs551415917	I>T	A:208	(-11.07, 2.10, 20.27)
16:88902256		E>A	A:212	(-8.26, -2.33, 23.62)
16:88902253		A>V	A:213	(-4.16, -0.49, 25.97)
16:88902254		A>S	A:213	(-4.16, -0.49, 25.97)
16:88902250		L>P	A:214	(-5.45, 1.71, 28.97)
16:88902244		F>S	A:216	(-3.44, -5.97, 27.96)
16:88902229		A>G	A:221	(-0.87, -5.83, 36.33)
16:88902226	rs140162658	R>Q	A:222	(0.04, -7.14, 41.51)
16:88902227	rs146963745	R>W	A:222	(0.04, -7.14, 41.51)
16:88902206	rs151165725	Y>H	A:229	(2.61, -4.75, 17.85)
16:88902194		D>N	A:233	(-3.34, 3.29, 11.26)
16:88902190		A>G	A:234	(-4.03, 7.42, 11.73)
16:88902182	rs550139020	A>T	A:237	(-3.67, 7.19, 4.13)
16:88902176	rs145131011	V>I	A:239	(-5.59, 10.84, 7.83)
16:88902163		K>T	A:243	(-15.09, 16.08, 16.96)
16:88902161		P>S	A:244	(-11.70, 16.26, 19.86)
16:88902151		G>D	A:247	(-8.19, 21.43, 13.89)
16:88902149		T>A	A:248	(-5.99, 21.08, 16.66)
16:88902133		R>Q	A:253	(-7.09, 15.39, 7.99)
16:88902134		R>W	A:253	(-7.09, 15.39, 7.99)
16:88901751		D>E	A:256	(-5.04, 16.55, 13.66)
16:88901749		A>V	A:257	(-3.23, 12.36, 14.25)
16:88901750		A>T	A:257	(-3.23, 12.36, 14.25)
16:88901747	COSM294397	V>I	A:258	(0.45, 13.22, 15.32)
16:88901737		I>T	A:261	(-0.99, 9.11, 18.33)
16:88901713		L>P	A:269	(3.41, 6.57, 29.68)
16:88901705		L>F	A:272	(2.68, 2.39, 33.18)
16:88901686	rs141544939	A>V	A:278	(7.22, 1.91, 35.17)
16:88901687	rs377591464	A>T	A:278	(7.22, 1.91, 35.17)
16:88901672		V>I	A:283	(8.66, 1.75, 26.47)
16:88901669	rs144067930	F>V	A:284	(11.52, 1.54, 21.42)
16:88901662	rs137927658	T>M	A:286	(9.35, 3.38, 15.96)
16:88901659	COSM3356878 CM970593	S>L	A:287	(8.21, 4.01, 12.35)
16:88901642		L>V	A:293	(6.34, 12.57, 0.67)
16:88901635	rs149239881	S>F	A:295	(0.12, 12.22, 0.99)
16:88901632	rs200371805	A>V	A:296	(1.92, 15.66, 1.09)
16:88901627		E>K	A:298	(-3.34, 18.04, 4.45)
16:88898507	rs118204443	G>C	A:301	(4.93, 13.90, 6.47)
16:88898497		G>V	A:304	(13.45, 16.56, 7.30)
16:88898498		G>S	A:304	(13.45, 16.56, 7.30)
16:88898494	COSM1709507	P>R	A:305	(16.89, 16.42, 7.09)
16:88898495		P>S	A:305	(16.89, 16.42, 7.09)
16:88898491		F>C	A:306	(17.06, 12.97, 6.31)
16:88898473	rs118204446	T>S	A:312	(12.86, 5.18, -1.03)
16:88898467		F>S	A:314	(17.24, 7.60, -1.09)
16:88898468		F>V	A:314	(17.24, 7.60, -1.09)
16:88898459	rs556060696	G>R	A:317	(12.57, 5.98, 4.16)
16:88898455		M>R	A:318	(14.63, 3.04, 5.79)
16:88898456	rs537013895	M>L	A:318	(14.63, 3.04, 5.79)
16:88898452	rs377744312	R>K	A:319	(17.49, 8.12, 9.54)
16:88898447		P>S	A:321	(11.60, 7.86, 14.86)
16:88898422		H>P	A:329	(16.25, 0.26, 34.54)
16:88898423		H>Y	A:329	(16.25, 0.26, 34.54)
16:88898420		V>I	A:330	(17.02, 3.99, 30.56)
16:88898413		A>V	A:332	(17.45, 10.42, 31.49)
16:88898414	rs375029033	A>T	A:332	(17.45, 10.42, 31.49)
16:88898407	rs138555898	Q>R	A:334	(20.97, 10.67, 27.67)
16:88893197		A>V	A:351	(17.03, -10.09, 26.57)
16:88893191		A>V	A:353	(13.15, -12.07, 29.08)
16:88893188		G>D	A:354	(16.03, -14.11, 29.32)
16:88893179		P>L	A:357	(18.11, -15.72, 20.01)
16:88893176		P>L	A:358	(16.65, -18.10, 17.20)
16:88893171	rs202031547	D>N	A:360	(17.74, -22.46, 13.73)
16:88893168		R>G	A:361	(16.35, -19.41, 12.46)
16:88893161	rs199663650	I>T	A:363	(19.02, -13.36, 13.94)
16:88893162		I>V	A:363	(19.02, -13.36, 13.94)
16:88893149	rs150111302	N>S	A:367	(21.25, -7.09, 22.60)
16:88893144	rs368784505	L>F	A:369	(20.31, -4.28, 26.81)
16:88893141		P>S	A:370	(24.48, -2.92, 25.85)
16:88893129		Q>E	A:374	(26.03, -0.50, 29.81)
16:88893122	rs150734270	R>Q	A:376	(28.87, -0.58, 26.38)
16:88893115	rs199850676	M>I	A:378	(27.52, -2.00, 18.94)
16:88893114	rs146471218	D>N	A:379	(30.67, -1.45, 13.99)
16:88891273	rs145583190	I>V	A:382	(22.20, -0.49, 8.20)
16:88891266		Y>C	A:384	(19.64, 1.00, 3.51)
16:88891261	rs118204437	R>C	A:386	(13.19, -0.87, -3.86)
16:88891253		D>E	A:388	(15.33, -8.54, -5.32)
16:88891255	rs373739301 CM042060	D>N	A:388	(15.33, -8.54, -5.32)
16:88891251		T>M	A:389	(17.67, -5.37, -4.41)
16:88891246	rs398123429 CM970603	M>V	A:391	(19.41, -0.60, -3.16)
16:88891242	rs398123430 CM042061	A>V	A:392	(22.22, 0.18, 0.49)
16:88891240	rs2303269	A>S	A:393	(25.10, 0.31, 2.94)
16:88891236		T>I	A:394	(25.40, 2.24, 6.50)
16:88891234		L>F	A:395	(29.56, 0.88, 8.08)
16:88891231	rs371459975	G>R	A:396	(28.97, 4.69, 10.25)
16:88891219	rs2303270	A>T	A:400	(26.61, 2.78, -0.16)
16:88891198		N>H	A:407	(9.41, 6.59, -9.52)
16:88891186	rs549276063	N>Y	A:411	(4.73, 5.99, -12.28)
16:88891181		F>L	A:412	(7.51, 11.95, -12.24)
16:88891179	rs374798170	R>K	A:413	(6.15, 11.41, -17.31)
16:88889114	rs142822371	I>T	A:416	(3.40, 9.35, -8.58)
16:88889102		P>L	A:420	(8.57, 16.16, -3.10)
16:88889085		G>R	A:426	(22.43, 11.06, -10.24)
16:88889079		T>A	A:428	(17.26, 11.51, -7.62)
16:88889075		T>I	A:429	(17.20, 8.26, -10.69)
16:88889076	rs554367594	T>A	A:429	(17.20, 8.26, -10.69)
16:88889070		N>D	A:431	(15.99, 4.88, -14.58)
16:88889058	rs375196202	H>Y	A:435	(25.54, 2.82, -9.12)
16:88889054		T>M	A:436	(27.40, -2.65, -8.50)
16:88889033		H>P	A:443	(30.06, 11.70, 5.83)
16:88889025	rs557217245	R>W	A:446	(30.73, 15.45, 5.82)
16:88889009		R>M	A:451	(22.00, 17.76, -0.68)
16:88889001	rs145767004	L>F	A:454	(32.30, 10.88, -1.73)
16:88884530		F>S	A:456	(34.14, 7.94, -7.79)
16:88884521	rs114703967	A>V	A:459	(40.69, 8.04, 0.28)
16:88884522		A>T	A:459	(40.69, 8.04, 0.28)
16:88884519		E>K	A:460	(36.50, 9.39, 2.55)
16:88884495	rs548706996	I>V	A:468	(30.72, -0.94, 2.91)
16:88884491		T>I	A:469	(32.29, -4.24, 0.05)
16:88884488		S>L	A:470	(33.45, -6.67, 3.47)
16:88884483	rs147290567	V>I	A:472	(27.86, -6.65, 1.46)
16:88884480	rs118204439 CM950542	Q>E	A:473	(31.24, -9.63, -0.22)
16:88884474		H>N	A:475	(24.53, -10.34, 3.94)
16:88884465		A>S	A:478	(25.44, -16.24, 4.20)
16:88884459	rs151296605	V>F	A:480	(19.77, -18.58, 1.60)
16:88884453		A>T	A:482	(13.44, -16.85, 0.96)
16:88884435	rs78127134	V>M	A:488	(0.66, -14.86, -5.87)
16:88884422	rs141171091	A>V	A:492	(-10.91, -14.95, -3.99)
16:88880927	COSM1609780	A>S	A:497	(-15.93, -14.38, 4.60)
16:88880920	rs542835085	P>L	A:499	(-13.98, -15.32, 10.61)
16:88880903		G>R	A:505	(-24.56, -11.03, 8.16)
16:88880885	rs530773540	P>A	A:511	(-15.14, -13.58, -6.96)
16:88880876	rs201153945	I>V	A:514	(-7.19, -17.73, -11.46)

4FDJ.A | GALNS.

4FDJ.A | GALNS

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
16:88902190	COSM2922622	A>V	A:234	(-4.03, 7.42, 11.73)
16:88901747	COSM294397	V>I	A:258	(0.45, 13.22, 15.32)
16:88880888	COSM32691	P>T	A:510	(-17.04, -14.80, -3.60)