4IQR.B | HNF4A

General Structure Information

PDB ID	4iqr
HGNC Gene Label(s)	HNF4A
Structure Name	multi-domain organization of the hnf4alpha nuclear receptor complex on dna
Resolution	2.9Å
Reference	AUTH V.CHANDRA,P.HUANG,N.POTLURI,D.WU,Y.KIM,F.RASTINEJADTITL MULTIDOMAIN INTEGRATION IN THE STRUCTURE OF THE HNF-4 ALPHATITL 2 NUCLEAR RECEPTOR COMPLEX.REF NATURE V. 495 394 2013REFN ISSN 0028-0836PMID 23485969DOI 10.1038/NATURE11966

Variant Set Distributions

ExAC Variants

Number Of Residues	308
Number Of SNVs	58
Number Of Permutations	63451
Optimal Distance Threshold	18.0
K Statistic	0.153
p-value	0.028

ClinVar

Number Of Residues	308
Number Of SNVs	7
Number Of Permutations	6812
Optimal Distance Threshold	35.0
K Statistic	0.762
p-value	0.661

COSMIC

Number Of Residues	308
Number Of SNVs	4
Number Of Permutations	941
Optimal Distance Threshold	35.0
K Statistic	0.333
p-value	0.8

Ripley’s K Analysis Plots

ExACClinVarCOSMIC

Variant Set Comparisons

ClinVar vs. ExAC

Number Of ExAC SNVs	58
Number Of ClinVar SNVs	7
Optimal Distance Threshold	12.0
K Statistic	0.077
p-value	0.472

Cosmic vs. ExAC

Pathogenic Proximity Analysis

ClinVar PathProx Analysis

COSMIC PathProx Analysis

Mapped Variants

[+] ExAC Missense Variants

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
20:43034772		G>R	B:55	(68.01, 1.19, 85.78)
20:43034779	rs561302824	R>Q	B:57	(67.77, 8.43, 80.56)
20:43034785	COSM188396 COSM188397	T>M	B:59	(62.01, 6.43, 77.41)
20:43034844	rs369182343 COSM577684 COSM1142854 COSM577685	V>M	B:79	(57.11, -12.04, 73.02)
20:43034851		K>R	B:81	(61.52, -13.97, 68.80)
20:43036029	rs371557531	R>Q	B:91	(66.57, -19.24, 88.85)
20:43036095		R>Q	B:113	(59.93, -9.81, 88.44)
20:43042336	rs377476335 COSM356496 COSM356497 CM022020	V>I	B:121	(53.75, -7.49, 72.24)
20:43042354	rs137853336	R>W	B:127	(59.10, -2.62, 54.38)
20:43042355	rs149611886	R>Q	B:127	(59.10, -2.62, 54.38)
20:43042361		S>T	B:129	(63.60, 1.14, 54.73)
20:43042363		T>A	B:130	(63.60, 4.29, 52.30)
20:43042364	rs1800961	T>I	B:130	(63.60, 4.29, 52.30)
20:43042367		R>Q	B:131	(67.32, 3.08, 51.18)
20:43042372		S>P	B:133	(68.45, -2.75, 46.93)
20:43042375	rs193922472	S>G	B:134	(66.51, -6.35, 46.48)
20:43042421	COSM1027074 COSM1592633 COSM1027075	A>V	B:149	(63.58, 2.95, 20.62)
20:43043184	rs142883089	R>Q	B:168	(48.01, 30.20, 15.81)
20:43043187	rs371827863 COSM1027078 COSM1153933	A>V	B:169	(51.19, 28.34, 11.63)
20:43043201		S>G	B:174	(46.37, 17.13, 1.47)
20:43043207		A>T	B:176	(49.07, 14.28, -0.50)
20:43043219		E>Q	B:180	(53.96, 13.20, 1.86)
20:43043243		V>I	B:188	(59.80, 5.49, 11.51)
20:43043282		E>K	B:201	(66.97, -12.33, 18.36)
20:43043289	rs201749293	P>L	B:203	(63.32, -14.88, 11.60)
20:43043297		D>N	B:206	(59.02, -14.06, 11.09)
20:43047080		A>S	B:213	(50.14, -6.84, 10.92)
20:43047129		V>A	B:229	(49.41, 18.44, 23.12)
20:43047138		D>V	B:232	(39.55, 19.57, 18.54)
20:43048364		N>S	B:238	(54.17, 16.43, 7.44)
20:43048372		I>V	B:241	(46.99, 20.62, 10.50)
20:43048381	rs376013528 CM082885	R>W	B:244	(36.26, 17.66, 14.81)
20:43048400	rs145542196	A>V	B:250	(35.90, 14.46, 2.57)
20:43048411		R>W	B:254	(32.96, 9.76, 8.48)
20:43048412	rs200985945 COSM3405114 COSM3405116 COSM3405115	R>L	B:254	(32.96, 9.76, 8.48)
20:43048414	rs139779712	V>M	B:255	(38.89, 8.69, 10.16)
20:43048435		E>K	B:262	(36.97, 6.88, 19.44)
20:43048451		F>S	B:267	(45.89, 8.75, 24.77)
20:43048457		E>A	B:269	(40.35, 11.74, 29.78)
20:43048458	rs193922477	E>D	B:269	(40.35, 11.74, 29.78)
20:43048484		A>G	B:278	(55.90, 2.07, 24.65)
20:43048487		Y>F	B:279	(55.34, -0.74, 28.33)
20:43048493	COSM577676 COSM1142858 COSM577677	K>R	B:281	(54.36, 0.77, 19.87)
20:43052672	rs201777208	S>G	B:294	(57.50, -19.35, 12.79)
20:43052675	rs145902391	D>N	B:295	(57.52, -19.55, 17.22)
20:43052689		I>M	B:299	(55.76, -13.62, 19.73)
20:43052693		R>W	B:301	(57.26, -16.90, 24.88)
20:43052706		Q>L	B:305	(58.00, -9.93, 29.12)
20:43052713		Q>H	B:307	(50.91, -7.80, 29.91)
20:43052719		S>R	B:309	(55.57, -4.65, 32.59)
20:43052742	COSM3405117 COSM3405119 COSM3405118	R>H	B:317	(53.12, 4.78, 39.07)
20:43052747		Y>H	B:319	(48.37, 7.47, 45.13)
20:43052756	rs193922479 COSM1027086 COSM1153934 CM064051	R>C	B:322	(40.55, 0.86, 40.97)
20:43052757	rs369429452	R>H	B:322	(40.55, 0.86, 40.97)
20:43052769		G>V	B:326	(42.02, -1.22, 31.15)
20:43052819		I>V	B:343	(42.52, 0.40, 5.22)
20:43052822	COSM1713520 COSM1713522 COSM1713521	E>Q	B:344	(37.41, -0.02, 3.70)
20:43052843		L>V	B:351	(39.11, 1.52, -7.04)
20:43052846		F>L	B:352	(37.08, 5.20, -7.47)
20:43052849	rs555432665	G>S	B:353	(41.75, 7.85, -8.78)
20:43052852		M>V	B:354	(42.60, 10.95, -5.86)
20:43052861		I>V	B:357	(48.60, 4.42, -3.11)
20:43052862		I>T	B:357	(48.60, 4.42, -3.11)
20:43052868		N>S	B:359	(54.63, 0.77, -3.71)

Position	Variant	AA Change	PDB Chain Position	Structure Coordinates
20:43034754	COSM4098688	A>T	B:49	(64.06, 8.21, 85.11)
20:43036063	COSM1681695	Q>H	B:102	(75.73, -11.11, 81.88)
20:43042336	COSM356497	V>L	B:121	(53.75, -7.49, 72.24)
20:43042421	COSM1592633	A>V	B:149	(63.58, 2.95, 20.62)
20:43048506	COSM1592631	F>L	B:285	(55.42, -5.19, 16.65)
20:43052754	COSM1027084	S>L	B:321	(45.92, 2.46, 39.37)

4IQR.B | HNF4A.

4IQR.B | HNF4A

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