PolyPhen: results for dnSNP rs5247

PolyPhen report

New Prediction

Citation

Help

refSNP	Predictions found for proteins:
rs5247	P23946

Acc number	Position	AA₁	AA₂	Description
P23946	66	H	R	Chymase precursor (EC 3.4.21.39) (Mast cell protease I). LENGTH: 247 AA

This variant is predicted to be probably damaging

Prediction	Available data	Prediction basis	Substitution effect	Prediction data
probably damaging	FT alignment structure	sequence annotation	2.2: functional effect, functional site Disruption of annotated functional site	site type: ACT_SITE
Remarks
Closest contact with ligand: PMS, distance 2.907
Closest contact with functional site: ASP 102A, distance 2.504 Å
Closest contact with other chains: CH2 5I, distance 1.471 Å

Sequence features of the substitution site

Region	Site	Feature table	Critical sites
N/A	ACT_SITE	show FT fields for P23946	66, 110, 203

PSIC profile scores for two amino acid variants

Score1	Score2	\|Score1-Score2\|	Observations	Diagnostics	Multiple alignment around substitution position
+2.811	-0.306	3.117	62	precomputed	Sequences: Flanks:

Mapping of the substitution site to known protein 3D structures

Database	Initial number of structures	Number of structures
PQS	501	16

Num	ID		Res	AA	E-value	Len	Ide	Gaps	Params	Cont	PDB TITLE
1	1klt	_	57	H	9.4e-133	226	1.00		Params	Het Site	N/A
2	1nn6	A	60	H	2.0e-130	224	1.00	2		Site	HUMAN PRO-CHYMASE
3	1pjp	A	57	H	6.1e-132	226	0.99			Chain Site	COMPLEX WITH SUCCINYL-ALA-ALA-PRO-PHE-CHLOROMETHYLKETONE
4	3rp2	B	57	H	8.1e-76	223	0.60			Site	N/A
5	3rp2	A	57	H	8.1e-76	223	0.60			Site	N/A
6	1euf	B	57	H	1.4e-64	225	0.56	2		Chain Site	BOVINE DUODENASE(NEW SERINE PROTEASE), CRYSTAL STRUCTURE
7	1euf	A	57	H	1.4e-64	225	0.56	2		Chain Site	BOVINE DUODENASE(NEW SERINE PROTEASE), CRYSTAL STRUCTURE
8	1iau	A	57	H	1.8e-59	228	0.54	7		Chain Site	HUMAN GRANZYME B IN COMPLEX WITH AC-IEPD-CHO
9	1kyn_2	A	57	H	2.5e-61	225	0.53	3		Het Site	CATHEPSIN-G
10	1fq3	B	57	H	5.2e-59	228	0.53	7		Site	CRYSTAL STRUCTURE OF HUMAN GRANZYME B
11	1fq3	A	57	H	5.2e-59	228	0.53	7		Site	CRYSTAL STRUCTURE OF HUMAN GRANZYME B
12	1fi8	B	57	H	3.9e-62	226	0.52	2		Chain Site	RAT GRANZYME B [N66Q] COMPLEXED TO ECOTIN [81-84 IEPD]
13	1kyn_1	B	357	H	1.9e-61	226	0.52	3		Het Site	CATHEPSIN-G
14	1cgh	A	57	H	1.9e-61	226	0.52	3		Chain Site	HUMAN CATHEPSIN G
15	1au8	A	57	H	1.9e-61	226	0.52	3		Chain Site	HUMAN CATHEPSIN G
16	1fi8	A	57	H	5.6e-61	226	0.52	3		Chain Site	RAT GRANZYME B [N66Q] COMPLEXED TO ECOTIN [81-84 IEPD]

Structural parameters

Num	ID		Res	SecStr	Acc	Acc Normed	dPropens	(Phi, Psi)	Map Region	dVol	Normed B-factor
1	1klt	_	57	G	94	0.55	1.03	(-70.6, -3.9)	A	20	0.24

Num	ID		Res	Heteroatoms	Interchain	Critical sites
1	1klt	_	57	`0.000Å`		`102_ ASP 2.954Å` `195_ SER 4.357Å`
2	1nn6	A	60			`104A ASP 2.819Å` `197A SER 2.689Å`
3	1pjp	A	57		`4I PRO 3.575Å` `0.000Å`	`102A ASP 2.831Å` `195A SER 2.747Å`
4	3rp2	B	57			`102B ASP 2.815Å` `195B SER 2.843Å`
5	3rp2	A	57			`102A ASP 2.917Å` `195A SER 3.073Å`
6	1euf	B	57		`36BA SER 3.263Å` `36CA GLY 4.172Å`	`102B ASP 2.603Å` `195B SER 3.173Å`
7	1euf	A	57		`36BB SER 3.263Å` `36CB GLY 4.172Å`	`102A ASP 2.603Å` `195A SER 3.173Å`
8	1iau	A	57		`404B PRO 3.324Å` `405B ASA 4.075Å`	`102A ASP 2.965Å` `195A SER 3.956Å`
9	1kyn_2	A	57	`601A KTP 3.286Å`		`102A ASP 2.619Å` `195A SER 2.605Å`
10	1fq3	B	57			`102B ASP 2.620Å` `195B SER 3.386Å`
11	1fq3	A	57			`0.000Å` `195A SER 3.324Å`
12	1fi8	B	57		`52E LEU 5.178Å` `83E PRO 3.569Å` `84E ASP 3.523Å`	`102B ASP 2.579Å` `195B SER 3.423Å`
13	1kyn_1	B	357	`701B KTP 3.478Å`		`402B ASP 2.974Å` `495B SER 2.782Å`
14	1cgh	A	57		`3S PRO 3.382Å` `4S PPH 2.837Å`	`102A ASP 2.722Å` `195A SER 3.075Å`
15	1au8	A	57		`3S PRO 3.243Å` `4S KPH 2.797Å`	`102A ASP 2.683Å` `195A SER 3.075Å`
16	1fi8	A	57		`52C LEU 5.298Å` `83C PRO 3.703Å` `84C ASP 3.481Å`	`102A ASP 2.591Å` `195A SER 3.421Å`