1GGU.B | F13A1

General Structure Information

PDB ID	1ggu
HGNC Gene Label(s)	F13A1
Structure Name	human factor xiii with calcium bound in the ion site
Resolution	2.1Å
Reference	AUTH B.A.FOX,V.C.YEE,L.C.PEDERSEN,I.LE TRONG,P.D.BISHOP,AUTH 2 R.E.STENKAMP,D.C.TELLERTITL IDENTIFICATION OF THE CALCIUM BINDING SITE AND ATITL 2 NOVEL YTTERBIUM SITE IN BLOOD COAGULATION FACTORTITL 3 XIII BY X-RAY CRYSTALLOGRAPHY.REF J.BIOL.CHEM. V. 274 4917 1999REFN ISSN 0021-9258PMID 9988734DOI 10.1074/JBC.274.8.4917

Variant Set Distributions

ExAC Variants

Number Of Residues	707
Number Of SNVs	174
Number Of Permutations	63790
Optimal Distance Threshold	30.0
K Statistic	0.321
p-value	0.002

ClinVar

Number Of Residues	707
Number Of SNVs	12
Number Of Permutations	5084
Optimal Distance Threshold	36.0
K Statistic	0.682
p-value	0.326

COSMIC

Number Of Residues	707
Number Of SNVs	18
Number Of Permutations	30131
Optimal Distance Threshold	39.0
K Statistic	0.425
p-value	0.168

Ripley’s K Analysis Plots

ExACClinVarCOSMIC

Variant Set Comparisons

ClinVar vs. ExAC

Number Of ExAC SNVs	174
Number Of ClinVar SNVs	12
Optimal Distance Threshold	36.0
K Statistic	0.234
p-value	0.141

Cosmic vs. ExAC

Number Of ExAC SNVs	174
Number Of COSMIC SNVs	14
Optimal Distance Threshold	11.0
K Statistic	-0.022
p-value	0.785

Pathogenic Proximity Analysis

ClinVar PathProx Analysis

COSMIC PathProx Analysis

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
6:6318864		R>G	B:11	(31.88, 13.14, 11.10)
6:6318857		A>V	B:13	(39.50, 15.33, 8.73)
6:6318839		S>C	B:19	(44.70, 4.41, 20.54)
6:6318830	COSM1546995	A>V	B:22	(48.49, 3.59, 18.06)
6:6318818		L>P	B:26	(57.16, 11.09, 13.34)
6:6318801		Q>K	B:32	(58.67, 22.84, 2.71)
6:6318797	COSM310975	G>V	B:33	(61.71, 23.73, -0.71)
6:6318794	rs540456397	V>A	B:34	(65.18, 24.38, -1.24)
6:6318791	COSM3830914	V>G	B:35	(68.62, 24.35, -1.29)
6:6305761		V>I	B:47	(70.98, 12.38, 18.31)
6:6305757	rs143616920	T>M	B:48	(74.46, 10.09, 19.66)
6:6305752		V>I	B:50	(68.78, 9.35, 24.83)
6:6305731		W>R	B:57	(69.26, 3.10, 40.80)
6:6305715		V>A	B:62	(62.46, 7.62, 43.71)
6:6305676		I>T	B:75	(57.23, 5.49, 34.93)
6:6305670	COSM597366 COSM1643125 CM040029	R>H	B:77	(53.58, 10.33, 38.93)
6:6305631		R>H	B:90	(77.84, 19.43, 17.06)
6:6305632		R>C	B:90	(77.84, 19.43, 17.06)
6:6305621		D>E	B:93	(76.58, 26.23, 19.59)
6:6305619		P>L	B:94	(74.00, 28.01, 22.15)
6:6267039	rs145761347	R>H	B:107	(46.92, 5.74, 13.83)
6:6267040	COSM2155235	R>C	B:107	(46.92, 5.74, 13.83)
6:6267023		N>K	B:112	(45.06, 21.51, 18.71)
6:6267019		G>R	B:114	(47.85, 17.01, 23.20)
6:6267009		I>T	B:117	(54.01, 17.37, 23.43)
6:6267004		V>M	B:119	(59.48, 20.30, 24.88)
6:6266997		I>T	B:121	(64.94, 24.48, 25.17)
6:6266998	rs142064728	I>V	B:121	(64.94, 24.48, 25.17)
6:6266987	rs147577601	E>D	B:124	(64.30, 28.98, 34.33)
6:6266984		L>F	B:125	(61.29, 25.14, 34.46)
6:6266977	COSM1547001	G>R	B:128	(52.40, 24.26, 34.06)
6:6266965	rs141030077	A>S	B:132	(63.33, 22.10, 28.89)
6:6266931	rs142954620	R>Q	B:143	(71.90, 16.48, 32.66)
6:6266905		C>S	B:152	(49.10, 15.69, 30.71)
6:6266901	rs542893144	I>T	B:153	(47.28, 13.12, 28.00)
6:6266892		K>R	B:156	(53.38, 4.33, 26.59)
6:6266887		R>C	B:158	(55.48, 8.00, 20.30)
6:6266872		V>L	B:163	(67.11, 19.39, 14.63)
6:6266862		P>L	B:166	(66.09, 26.52, 7.94)
6:6266859		Y>C	B:167	(66.35, 24.32, 4.86)
6:6266854	rs140712764	V>I	B:169	(62.71, 18.97, 10.85)
6:6266847	rs376147795 COSM43061	R>Q	B:171	(62.10, 14.07, 13.79)
6:6266838	rs538605561 COSM3629132	R>Q	B:174	(59.75, 4.21, 17.72)
6:6266835		N>S	B:175	(63.62, 4.25, 20.68)
6:6266833		P>S	B:176	(61.02, 1.56, 21.70)
6:6266820		T>M	B:180	(57.69, 8.05, 28.59)
6:6266792		E>D	B:189	(50.54, 22.48, 44.22)
6:6266794		E>K	B:189	(50.54, 22.48, 44.22)
6:6251154		V>M	B:193	(44.69, 14.16, 41.64)
6:6251150		Y>C	B:194	(47.52, 18.03, 45.96)
6:6251151		Y>H	B:194	(47.52, 18.03, 45.96)
6:6251148	COSM1547005	L>M	B:195	(46.28, 14.00, 48.31)
6:6251129	rs146801542	R>K	B:201	(50.33, 11.57, 49.04)
6:6251123		E>G	B:203	(46.55, 3.87, 51.83)
6:6251124		E>K	B:203	(46.55, 3.87, 51.83)
6:6251120	rs3024477	Y>F	B:204	(43.88, 6.60, 50.01)
6:6251117		V>A	B:205	(48.41, 5.93, 45.46)
6:6251118		V>I	B:205	(48.41, 5.93, 45.46)
6:6251097		I>V	B:212	(37.12, -6.00, 51.04)
6:6251090	rs373039706	Y>F	B:214	(32.70, -9.73, 54.34)
6:6251085		E>Q	B:216	(25.91, -8.01, 59.47)
6:6248639		I>N	B:234	(48.65, -4.11, 35.54)
6:6248610		R>G	B:244	(38.87, -3.04, 24.02)
6:6248600	rs577966272 COSM3922050	M>T	B:247	(39.30, 7.23, 26.11)
6:6248597		D>V	B:248	(39.66, 10.91, 23.27)
6:6248591		S>Y	B:250	(42.01, 14.31, 24.76)
6:6248570	rs142092590	K>R	B:257	(36.35, 11.26, 30.60)
6:6248561	rs121913071	R>H	B:260	(31.25, 8.40, 33.65)
6:6225093	rs537101736	V>M	B:266	(34.36, -2.96, 35.06)
6:6225075	COSM1080881	E>K	B:272	(32.94, -5.00, 24.98)
6:6225048		N>D	B:281	(25.23, -20.13, 44.10)
6:6225035		Y>C	B:285	(30.97, -23.24, 31.54)
6:6225030	rs370205818	V>I	B:287	(35.75, -18.02, 38.40)
6:6225026		P>R	B:288	(33.69, -18.34, 41.48)
6:6225027	rs201752338	P>T	B:288	(33.69, -18.34, 41.48)
6:6225023	COSM1445524 COSM3629118 CM103179	P>Q	B:289	(32.82, -14.24, 42.35)
6:6225024		P>A	B:289	(32.82, -14.24, 42.35)
6:6225005	rs535694758	S>N	B:295	(43.02, -7.51, 40.16)
6:6225003	rs199564311 COSM3411233	V>I	B:296	(46.42, -9.47, 38.85)
6:6225000		D>N	B:297	(44.17, -12.90, 38.09)
6:6224981	rs139164988	R>Q	B:303	(45.66, -7.75, 26.73)
6:6224982		R>W	B:303	(45.66, -7.75, 26.73)
6:6224969		N>S	B:307	(37.31, -11.77, 25.81)
6:6222398	rs121913072	R>Q	B:326	(45.26, 2.79, 44.29)
6:6222381		A>T	B:332	(41.56, 5.23, 45.65)
6:6222339		A>T	B:346	(15.65, 7.79, 42.95)
6:6222320		I>N	B:352	(7.87, -3.93, 53.29)
6:6222317	rs369083276	F>Y	B:353	(4.11, -4.81, 50.14)
6:6222315		L>V	B:354	(2.36, -6.22, 55.67)
6:6222312		E>Q	B:355	(-0.71, -10.36, 54.87)
6:6197534		W>R	B:379	(40.80, 13.31, 46.58)
6:6197506		G>E	B:388	(33.16, 21.89, 47.40)
6:6197488	rs76451285	A>V	B:394	(31.25, 8.30, 43.92)
6:6197459		D>N	B:404	(21.47, 7.23, 30.64)
6:6196109	rs532879106 COSM3629115 CM950378	R>Q	B:408	(28.33, 4.09, 34.85)
6:6196110	COSM1672216	R>W	B:408	(28.33, 4.09, 34.85)
6:6196098	rs139636536	A>T	B:412	(29.62, 11.64, 42.79)
6:6196064	rs371619552	C>Y	B:423	(21.86, 18.61, 40.15)
6:6196049	rs143513902	A>V	B:428	(23.62, 11.69, 42.53)
6:6182365	rs145376560	D>N	B:438	(12.95, 5.45, 53.95)
6:6182344		K>E	B:445	(-6.56, -4.56, 52.45)
6:6182331		T>I	B:449	(-6.69, -1.10, 48.99)
6:6182325		V>E	B:451	(-2.42, 0.74, 54.53)
6:6182326	rs373405542 COSM387628	V>M	B:451	(-2.42, 0.74, 54.53)
6:6182322		V>G	B:452	(1.00, 3.59, 55.40)
6:6182320	rs573785951	E>K	B:453	(0.99, 0.68, 58.76)
6:6182308		A>T	B:457	(14.71, 5.88, 58.57)
6:6182298		I>T	B:460	(18.98, 2.12, 54.21)
6:6182290		L>V	B:463	(27.91, 1.43, 58.59)
6:6182275	rs150455213	Q>K	B:468	(43.10, 1.90, 59.06)
6:6182253	rs375123237	M>R	B:475	(37.50, 4.69, 58.22)
6:6182240		D>E	B:479	(30.50, 11.56, 58.35)
6:6175098		Q>E	B:487	(19.14, 17.65, 64.08)
6:6175094	rs146866566	E>G	B:488	(18.33, 21.62, 59.62)
6:6175084		R>S	B:491	(15.01, 19.49, 57.01)
6:6175079		A>V	B:493	(19.47, 17.53, 52.24)
6:6175070		T>I	B:496	(17.77, 20.00, 48.28)
6:6175068		A>S	B:497	(17.04, 16.30, 46.78)
6:6175060		M>I	B:499	(14.25, 20.29, 44.80)
6:6175056	rs121913068	G>R	B:501	(15.75, 13.74, 41.73)
6:6175053	rs568468779	A>T	B:502	(14.67, 12.87, 44.64)
6:6175046		K>M	B:504	(9.50, 10.66, 49.36)
6:6175036		N>K	B:507	(2.46, 10.87, 52.53)
6:6175007	rs369134587	N>S	B:517	(3.06, 4.39, 72.72)
6:6175008		N>H	B:517	(3.06, 4.39, 72.72)
6:6175005		V>I	B:518	(4.47, -0.36, 71.36)
6:6174999	rs547064561	M>L	B:520	(9.97, -4.15, 68.21)
6:6174986		V>A	B:524	(20.33, -12.17, 65.96)
6:6174960		F>I	B:533	(20.86, -19.01, 65.66)
6:6174956	rs151032137	K>R	B:534	(19.07, -17.90, 70.74)
6:6174935		N>S	B:541	(3.99, -0.66, 76.89)
6:6174920	rs374508373 COSM3875050	R>H	B:546	(-3.62, -5.20, 78.93)
6:6174921	COSM1080876	R>C	B:546	(-3.62, -5.20, 78.93)
6:6174908	rs5984	T>I	B:550	(0.07, -11.26, 67.15)
6:6174906		A>T	B:551	(3.96, -11.92, 66.49)
6:6174896	rs201203914	S>L	B:554	(10.28, -14.74, 58.77)
6:6174893		A>G	B:555	(13.33, -16.88, 58.29)
6:6174884		T>N	B:558	(19.52, -14.67, 51.68)
6:6174872		G>E	B:562	(18.49, -9.99, 49.80)
6:6174873	rs121913069	G>R	B:562	(18.49, -9.99, 49.80)
6:6174866	rs5982	P>L	B:564	(14.83, -14.15, 49.00)
6:6174842	rs113599940	T>M	B:572	(3.11, -17.14, 65.47)
6:6174830	rs143711562	T>M	B:576	(-0.00, -9.70, 77.12)
6:6174815		S>F	B:581	(6.54, -2.86, 80.06)
6:6167833	rs5983	L>Q	B:588	(16.51, -22.15, 69.44)
6:6167822	rs138754417	G>S	B:592	(18.90, -27.89, 61.02)
6:6167819	rs529985469	E>K	B:593	(15.93, -24.96, 61.71)
6:6167795		Q>K	B:601	(28.19, -14.73, 51.29)
6:6167791	rs148207995	A>V	B:602	(25.64, -17.46, 54.85)
6:6167782		H>P	B:605	(16.20, -11.37, 56.54)
6:6167783	rs373723380	H>N	B:605	(16.20, -11.37, 56.54)
6:6167767		A>G	B:610	(3.38, -7.21, 64.93)
6:6167765	COSM3875047	R>C	B:611	(-1.90, -7.65, 64.75)
6:6167760		I>M	B:612	(-1.19, -3.86, 68.58)
6:6167749		R>M	B:616	(-6.24, -3.41, 64.51)
6:6167741		L>M	B:619	(5.05, -3.47, 65.63)
6:6167738	rs145180358	A>S	B:620	(8.29, -3.67, 62.24)
6:6167735	rs141416839	K>E	B:621	(12.13, -3.86, 63.20)
6:6167720	rs200830173	V>M	B:626	(26.43, -13.78, 58.37)
6:6167714		T>P	B:628	(31.18, -17.53, 60.79)
6:6167705		E>Q	B:631	(39.89, -18.28, 58.11)
6:6167695	rs372738301 COSM597381	I>T	B:634	(48.71, -19.04, 55.27)
6:6152178		R>H	B:637	(58.80, -23.17, 55.31)
6:6152179	rs200803360	R>C	B:637	(58.80, -23.17, 55.31)
6:6152169		Q>R	B:640	(61.03, -14.28, 55.10)
6:6152155		D>Y	B:645	(63.63, -19.61, 47.98)
6:6152137	rs5988	E>Q	B:651	(46.48, -25.80, 56.16)
6:6152125		P>S	B:655	(34.19, -27.39, 58.04)
6:6152110		L>V	B:660	(34.06, -30.44, 49.83)
6:6152106	COSM3159986	R>Q	B:661	(32.63, -33.50, 45.56)
6:6152091		H>R	B:666	(42.68, -19.43, 44.57)
6:6152089	rs570157317	L>V	B:667	(48.18, -18.26, 46.83)
6:6152085	rs375129902 COSM743395 CM103185	D>G	B:668	(47.84, -13.69, 45.99)
6:6152074		V>I	B:672	(55.42, -12.67, 47.35)
6:6152067		R>K	B:674	(51.74, -13.19, 39.28)
6:6152060	rs551878781	M>I	B:676	(49.12, -19.47, 42.05)
6:6152062	rs371964182	M>V	B:676	(49.12, -19.47, 42.05)
6:6152055	rs201302247	K>M	B:678	(46.16, -27.43, 43.82)
6:6152046	rs121913064 CS920751	R>L	B:681	(39.31, -34.23, 41.43)
6:6152047		R>C	B:681	(39.31, -34.23, 41.43)
6:6145997	rs184352526	R>Q	B:684	(35.53, -37.61, 51.77)
6:6145998	COSM3629111	R>W	B:684	(35.53, -37.61, 51.77)
6:6145967		V>A	B:694	(58.62, -21.99, 46.07)
6:6145961	COSM597384	R>Q	B:696	(62.72, -16.49, 44.22)
6:6145962		R>W	B:696	(62.72, -16.49, 44.22)
6:6145958		P>L	B:697	(60.36, -12.81, 47.19)
6:6145940	rs377484555 HM090014	R>Q	B:703	(54.05, -7.32, 51.06)
6:6145941	rs267606787 COSM3430819 CM093521	R>W	B:703	(54.05, -7.32, 51.06)
6:6145936		K>N	B:704	(49.39, -9.72, 53.16)
6:6145931		I>T	B:706	(46.08, -13.55, 49.90)
6:6145921	rs140537838	M>I	B:709	(37.82, -22.36, 49.32)
6:6145903	COSM1547010	R>S	B:715	(31.43, -20.95, 47.35)
6:6145904	rs147189258	R>K	B:715	(31.43, -20.95, 47.35)
6:6145905		R>G	B:715	(31.43, -20.95, 47.35)
6:6145898	COSM1621851	V>A	B:717	(36.77, -19.52, 52.14)
6:6145890	rs533127151	E>K	B:720	(45.60, -13.10, 55.78)
6:6145880		V>A	B:723	(55.14, -11.43, 55.38)
6:6145881		V>M	B:723	(55.14, -11.43, 55.38)
6:6145878		Q>K	B:724	(58.19, -8.63, 57.44)

1GGU.B | F13A1.

1GGU.B | F13A1

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
6:6318795	rs5985	V>L	B:34	(65.18, 24.38, -1.24)
6:6305720	rs121913067	N>K	B:60	(63.75, 10.23, 37.51)
6:6248615	rs267606788	M>T	B:242	(41.67, 3.56, 28.39)
6:6248561	rs121913071	R>H	B:260	(31.25, 8.40, 33.65)
6:6225041	rs121913074	Y>C	B:283	(28.98, -18.89, 39.88)
6:6224943	rs121913073	V>F	B:316	(35.15, -8.02, 42.15)
6:6222398	rs121913072	R>Q	B:326	(45.26, 2.79, 44.29)
6:6196092	rs121913070	V>F	B:414	(30.56, 12.61, 48.51)
6:6175056	rs121913068	G>R	B:501	(15.75, 13.74, 41.73)
6:6174873	rs121913069	G>R	B:562	(18.49, -9.99, 49.80)
6:6152046	rs121913064	R>L	B:681	(39.31, -34.23, 41.43)
6:6145941	rs267606787	R>W	B:703	(54.05, -7.32, 51.06)