2BB5.B | TCN2 – ASTRID

2BB5.B | TCN2

General Structure Information

PDB ID	2bb5
HGNC Gene Label(s)	TCN2
Structure Name	structure of human transcobalamin in complex with cobalamin
Resolution	3.2Å
Reference	AUTH J.WUERGES,G.GARAU,S.GEREMIA,S.N.FEDOSOV,T.E.PETERSEN,AUTH 2 L.RANDACCIOTITL STRUCTURAL BASIS FOR MAMMALIAN VITAMIN B12 TRANSPORT BYTITL 2 TRANSCOBALAMIN.REF PROC.NATL.ACAD.SCI.USA V. 103 4386 2006REFN ISSN 0027-8424PMID 16537422DOI 10.1073/PNAS.0509099103

Variant Set Distributions

ExAC Variants

Number Of Residues	409
Number Of SNVs	148
Number Of Permutations	20415
Optimal Distance Threshold	6.0
K Statistic	0.009
p-value	0.71

COSMIC

Number Of Residues	409
Number Of SNVs	3
Number Of Permutations	154
Optimal Distance Threshold	7.0
K Statistic	0.333
p-value	0.131

Ripley’s K Analysis Plots

ExACCOSMIC

Variant Set Comparisons

Cosmic vs. ExAC

Number Of ExAC SNVs	148
Number Of COSMIC SNVs	4
Optimal Distance Threshold	7.0
K Statistic	0.149
p-value	0.903

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
22:31003376	rs375476510	M>L	B:2	(71.96, 23.72, 50.55)
22:31003377		M>K	B:2	(71.96, 23.72, 50.55)
22:31006860	rs9606756	I>V	B:5	(61.63, 26.07, 49.45)
22:31006870		M>R	B:8	(54.96, 29.63, 51.34)
22:31006882	rs116605132	L>R	B:12	(48.79, 30.17, 49.37)
22:31006900		Q>R	B:18	(40.61, 24.70, 50.14)
22:31006923	rs374992877	R>W	B:26	(34.42, 13.07, 42.15)
22:31006924	COSM332863	R>Q	B:26	(34.42, 13.07, 42.15)
22:31006930		S>C	B:28	(34.74, 7.03, 40.14)
22:31006932	rs200833932	L>M	B:29	(37.24, 3.43, 38.32)
22:31006948		P>R	B:34	(46.62, 7.85, 43.11)
22:31006950		S>G	B:35	(48.61, 11.73, 43.06)
22:31006953	rs556464879	I>F	B:36	(45.14, 13.43, 45.00)
22:31006963		G>V	B:39	(49.76, 14.62, 48.41)
22:31006968		R>C	B:41	(49.12, 10.80, 54.04)
22:31006977	rs145474456	S>G	B:44	(50.60, 20.51, 55.74)
22:31006978		S>N	B:44	(50.60, 20.51, 55.74)
22:31007008		Y>C	B:54	(40.33, 8.65, 47.51)
22:31007023	rs75680863	K>M	B:59	(43.07, -0.57, 48.83)
22:31007028		G>C	B:61	(39.62, -0.99, 42.22)
22:31007029		G>D	B:61	(39.62, -0.99, 42.22)
22:31007041		C>Y	B:65	(40.12, -4.22, 38.00)
22:31007043		L>F	B:66	(44.65, -4.89, 37.70)
22:31007046	rs367867691	L>V	B:67	(43.35, -8.58, 40.89)
22:31007050	rs371944934	G>E	B:68	(39.84, -10.87, 38.59)
22:31008861		S>P	B:69	(38.38, -13.55, 36.11)
22:31008867	rs35915865	F>L	B:71	(40.66, -19.79, 34.41)
22:31008873	rs559879608	E>K	B:73	(33.71, -14.60, 30.78)
22:31008876	rs528704555	D>N	B:74	(36.08, -12.01, 28.01)
22:31008882	rs11557600	G>S	B:76	(35.82, -6.02, 27.01)
22:31008889	rs141635240	C>Y	B:78	(33.38, -3.63, 32.64)
22:31008894		G>S	B:80	(39.23, -0.27, 31.65)
22:31008898	rs150225103	K>T	B:81	(41.53, -2.63, 33.31)
22:31008901		P>L	B:82	(43.84, 0.54, 35.83)
22:31008906		M>V	B:84	(50.42, -0.85, 34.09)
22:31008915		L>V	B:87	(49.75, -0.03, 39.34)
22:31008916		L>P	B:87	(49.75, -0.03, 39.34)
22:31008933		A>T	B:93	(49.59, 5.26, 47.98)
22:31008934		A>V	B:93	(49.59, 5.26, 47.98)
22:31008936	COSM3553371	L>F	B:94	(49.92, 1.47, 49.44)
22:31008946		N>S	B:97	(49.06, 4.20, 54.92)
22:31008955	rs199728304	F>S	B:100	(55.40, -2.63, 52.22)
22:31008960		R>G	B:102	(50.73, -6.23, 52.84)
22:31008966	rs373115973	H>D	B:104	(48.69, -14.41, 46.99)
22:31008967		H>L	B:104	(48.69, -14.41, 46.99)
22:31008970	rs368757546	K>R	B:105	(46.05, -9.49, 46.40)
22:31008971		K>N	B:105	(46.05, -9.49, 46.40)
22:31008978	rs552020145	R>G	B:108	(48.20, -11.35, 40.70)
22:31008980		R>S	B:108	(48.20, -11.35, 40.70)
22:31008984		V>F	B:110	(54.61, -6.66, 41.79)
22:31008988	rs200868221 COSM345192	S>L	B:111	(54.24, -9.43, 38.50)
22:31008993		L>F	B:113	(54.71, -2.99, 37.34)
22:31009011		D>N	B:119	(56.70, -5.40, 27.73)
22:31009023		A>T	B:123	(60.01, -1.62, 22.74)
22:31009024	rs534564986	A>G	B:123	(60.01, -1.62, 22.74)
22:31009026	rs200771616 COSM382263	I>V	B:124	(63.42, 0.38, 23.59)
22:31009027	rs200483369	I>T	B:124	(63.42, 0.38, 23.59)
22:31010338		H>Y	B:126	(68.84, -2.19, 21.39)
22:31010355		H>Q	B:131	(60.24, 5.16, 20.49)
22:31010356		P>A	B:132	(58.55, 3.84, 24.79)
22:31010363		T>I	B:134	(54.20, 4.60, 27.43)
22:31010377	rs369762215 COSM1683120	Y>H	B:139	(60.99, 2.48, 32.01)
22:31010390		I>T	B:143	(61.93, 1.64, 38.15)
22:31010395		A>S	B:145	(57.48, 1.84, 42.55)
22:31010396		A>V	B:145	(57.48, 1.84, 42.55)
22:31010408	rs200303429	H>L	B:149	(56.46, -1.45, 47.55)
22:31010416	rs200135085	R>W	B:152	(66.01, -6.14, 43.60)
22:31010417	rs117353193	R>Q	B:152	(66.01, -6.14, 43.60)
22:31010419	COSM1682202	V>F	B:153	(64.36, -4.39, 38.47)
22:31010431	rs142791153	V>M	B:157	(65.04, -2.54, 33.10)
22:31010437		D>N	B:159	(70.42, -0.62, 31.27)
22:31010447	rs142651651	L>P	B:162	(70.90, 4.42, 32.77)
22:31010450	rs376685318	Y>C	B:163	(71.40, 5.36, 26.22)
22:31010455	rs201925682	V>M	B:165	(69.68, 10.51, 30.97)
22:31010461		P>T	B:167	(71.02, 12.21, 25.15)
22:31010462	rs146009793	P>L	B:167	(71.02, 12.21, 25.15)
22:31010465	rs139905684	F>S	B:168	(67.02, 10.84, 24.11)
22:31010474		G>D	B:171	(60.89, 19.48, 25.85)
22:31010476		H>Y	B:172	(57.43, 20.55, 28.50)
22:31010477		H>R	B:172	(57.43, 20.55, 28.50)
22:31010480	rs151172486	H>R	B:173	(56.98, 16.91, 28.33)
22:31011294		A>E	B:178	(64.34, 13.89, 34.44)
22:31011296		A>S	B:179	(62.79, 14.14, 37.61)
22:31011297		A>G	B:179	(62.79, 14.14, 37.61)
22:31011312		A>V	B:184	(64.45, 6.41, 40.56)
22:31011320		C>G	B:187	(65.54, 4.77, 45.27)
22:31011323		L>V	B:188	(67.75, 2.23, 42.87)
22:31011329		R>C	B:190	(68.71, 6.86, 49.41)
22:31011330	rs150472705	R>H	B:190	(68.71, 6.86, 49.41)
22:31011332		S>P	B:191	(68.88, 0.58, 48.68)
22:31011340		F>L	B:193	(67.57, -2.53, 45.08)
22:31011348	rs372458211	G>D	B:196	(76.22, -3.18, 38.58)
22:31011350	rs35838082	R>W	B:197	(74.60, -1.45, 36.18)
22:31011351		R>Q	B:197	(74.60, -1.45, 36.18)
22:31011359	COSM4137385	R>W	B:200	(75.99, 3.89, 34.35)
22:31011360	COSM4103471	R>Q	B:200	(75.99, 3.89, 34.35)
22:31011368		M>V	B:203	(77.57, 8.81, 36.66)
22:31011374	rs144889471	I>V	B:205	(71.75, 11.17, 39.91)
22:31011378	COSM1308068	R>T	B:206	(76.94, 15.03, 38.68)
22:31011380		T>A	B:207	(73.51, 13.78, 34.36)
22:31011392		E>K	B:211	(69.32, 17.75, 31.73)
22:31011395		I>F	B:212	(66.96, 19.93, 35.74)
22:31011404		A>T	B:215	(66.49, 24.45, 32.41)
22:31011407		Q>E	B:216	(66.50, 27.88, 36.06)
22:31011408	rs145641025	Q>P	B:216	(66.50, 27.88, 36.06)
22:31011426		F>Y	B:222	(63.53, 24.45, 37.34)
22:31011440		S>G	B:227	(57.99, 21.20, 35.41)
22:31011444	rs147738100	T>I	B:228	(59.00, 23.46, 38.94)
22:31011590	rs142553702	F>L	B:234	(65.97, 15.29, 41.67)
22:31011595		M>T	B:236	(64.21, 18.49, 47.73)
22:31011607	rs113331651	M>T	B:240	(76.54, 18.78, 46.02)
22:31011609	rs201501842	R>C	B:241	(76.85, 21.47, 48.42)
22:31011612		G>W	B:242	(78.38, 25.20, 47.41)
22:31011618	rs61743653	E>Q	B:244	(75.01, 26.05, 41.76)
22:31011621	rs201848801	L>V	B:245	(71.20, 23.74, 44.62)
22:31011643	rs201392026	A>V	B:252	(61.98, 28.88, 42.14)
22:31011689	rs376839271	N>K	B:267	(45.39, 20.24, 38.03)
22:31011691	rs149231407	A>V	B:268	(44.72, 18.24, 41.11)
22:31011693	rs369458782	L>F	B:269	(48.09, 15.92, 39.18)
22:31011696		M>V	B:270	(50.19, 19.95, 39.14)
22:31011699		I>V	B:271	(47.76, 20.77, 43.64)
22:31011717	COSM4103473	V>I	B:277	(57.68, 20.54, 47.57)
22:31011720	rs553954429	L>V	B:278	(54.93, 23.53, 49.66)
22:31011726		H>Y	B:280	(59.85, 20.97, 53.64)
22:31011727		H>R	B:280	(59.85, 20.97, 53.64)
22:31011728		H>Q	B:280	(59.85, 20.97, 53.64)
22:31011733		T>I	B:282	(60.06, 13.94, 48.47)
22:31011736		Y>C	B:283	(56.86, 11.35, 45.20)
22:31011738		I>V	B:284	(62.56, 9.59, 48.26)
22:31011739		I>T	B:284	(62.56, 9.59, 48.26)
22:31011750	COSM3553374	F>L	B:288	(62.48, 5.24, 55.43)
22:31013319		M>V	B:297	(41.66, 19.61, 59.36)
22:31013320		M>T	B:297	(41.66, 19.61, 59.36)
22:31013335		A>V	B:302	(31.89, 26.51, 51.34)
22:31013346	rs149299209	P>S	B:306	(29.25, 33.67, 43.16)
22:31013379		Q>E	B:317	(41.24, 26.59, 14.27)
22:31013397		P>A	B:323	(37.60, 19.58, 5.44)
22:31013408		R>S	B:326	(37.79, 28.72, 11.35)
22:31013410		Q>P	B:327	(32.29, 27.28, 13.94)
22:31013419	rs9621049	S>F	B:330	(29.18, 31.33, 22.14)
22:31013430		G>R	B:334	(34.91, 30.65, 32.26)
22:31013431		G>E	B:334	(34.91, 30.65, 32.26)
22:31013434	rs539987014	S>C	B:335	(34.20, 28.63, 29.95)
22:31013439		V>M	B:337	(38.41, 24.23, 26.08)
22:31013459		K>N	B:343	(28.64, 23.97, 23.69)
22:31013465		H>Q	B:345	(28.67, 17.46, 19.54)
22:31013472		G>R	B:348	(27.31, 20.82, 14.81)
22:31013482	rs376218060	T>I	B:351	(33.22, 15.10, 16.86)
22:31018959		E>K	B:353	(36.29, 10.93, 21.43)
22:31018972	rs150517433	S>F	B:357	(43.46, 11.09, 33.41)
22:31018975	rs1131603	L>S	B:358	(45.62, 10.70, 37.09)
22:31018976		L>F	B:358	(45.62, 10.70, 37.09)
22:31018983		P>S	B:361	(40.03, 15.34, 30.51)
22:31018987		Y>S	B:362	(44.64, 12.59, 26.49)
22:31018998	rs144166182	V>M	B:366	(39.40, 15.55, 16.51)
22:31019003		M>I	B:367	(36.31, 15.91, 13.14)
22:31019007		K>E	B:369	(42.14, 11.25, 13.05)
22:31019011	COSM184806	A>V	B:370	(42.41, 9.10, 16.10)
22:31019016	rs367605153 COSM725923	G>R	B:372	(48.20, 7.67, 16.83)
22:31019031		W>R	B:377	(44.58, 15.74, 17.90)
22:31019032		W>L	B:377	(44.58, 15.74, 17.90)
22:31019044	rs4820889	R>Q	B:381	(47.42, 30.81, 23.20)
22:31019053		N>S	B:384	(51.63, 28.76, 16.71)
22:31019061		L>V	B:387	(47.68, 25.33, 25.70)
22:31019067	COSM3939606	Q>K	B:389	(46.27, 24.67, 31.19)
22:31022449	rs371229602	I>V	B:391	(40.13, 20.39, 27.55)
22:31022450		I>S	B:391	(40.13, 20.39, 27.55)
22:31022453	rs145807876	A>G	B:392	(39.60, 21.26, 31.81)
22:31022456		D>G	B:393	(42.20, 23.15, 33.45)
22:31022459		Y>S	B:394	(42.92, 27.74, 28.52)
22:31022461	rs148963479	R>G	B:395	(38.83, 28.35, 32.62)
22:31022464		P>S	B:396	(39.13, 30.65, 27.18)
22:31022468		K>R	B:397	(40.28, 35.12, 27.81)
22:31022470		D>N	B:398	(36.44, 37.55, 24.10)
22:31022485		E>K	B:403	(45.03, 24.83, 16.49)
22:31022504	rs367829511	W>L	B:409	(55.74, 12.17, 20.86)

2BB5.B | TCN2.

2BB5.B | TCN2

General Structure Information

Variant Set Distributions

Ripley’s K Analysis Plots

Variant Set Comparisons

Mapped Variants

[+] ExAC Missense Variants

[+] COSMIC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
22:31006924	COSM4852174	R>Q	B:26	(34.42, 13.07, 42.15)
22:31011405	COSM1722784	A>V	B:215	(66.49, 24.45, 32.41)
22:31019011	COSM184806	A>V	B:370	(42.41, 9.10, 16.10)
22:31019016	COSM725923	G>R	B:372	(48.20, 7.67, 16.83)