Variant VAR_016411 | SNPeffect 4.0

Phenotypic summary of VAR_016411

Compact overview of VAR_016411
UniProt ID	Gene	Mutation	Mutation type	Disease	OMIM	dbSNP
1B38_HUMAN	HLA-B	S35A	Polymorphism	-	No OMIM entry	rs1131170

Short stretch summary of VAR_016411
Predictor	Predicted regions overview	Comparison to WT	Stretches in variant	Stretches in WT
Tango		53 Increased	6	5
Waltz		1 No change	2	2
Limbo		0 No change	5	5
Domain composition of 1B38_HUMAN
Database	Domain composition	Residue details
PFAM		MHC_I (Residues 25-203), C1-set (Residues 210-295), MHC_I_C (Residues 336-362)
SMART		IGc1 (Residues 222-293)

Structure stability summary of VAR_016411
Variant	Stability change	Effect	Structure	Stability frequency histogram
S35A	-1.03 kcal/mol	Enhanced stability

TANGO aggregation

Graphical comparison of TANGO regions in variant and wild type
Protein	Predicted regions overview	TANGO regions	Total score
Variant		6	3193
Wild type		5	3141

TANGO regions in wild type and variant
Wild type TANGO regions
N-term gatekeepers	TANGO region	C-term gatekeepers	Start	End	Score
VMAPR	TVLLLLSAALALT	ETWAG	8	20	87
RGEPR	FISVGYV	DDTQF	46	52	36
FYPAE	ITLTW	QRDGE	237	241	13
RTFQK	WAAVV	VPSGE	268	272	10
QSTVP	IVGIVAGLAVLAVVVIGAVVAAVM	CRRKS	308	331	68
Variant protein TANGO regions
N-term gatekeepers	TANGO region	C-term gatekeepers	Start	End	Score
VMAPR	TVLLLLSAALALT	ETWAG	8	20	87
SHSMR	YFYTAV	SRPGR	31	36	10
RGEPR	FISVGYV	DDTQF	46	52	36
FYPAE	ITLTW	QRDGE	237	241	13
RTFQK	WAAVV	VPSGE	268	272	10
QSTVP	IVGIVAGLAVLAVVVIGAVVAAVM	CRRKS	308	331	68

Difference in TANGO aggregation between wild type and variant
	This graph plots the per-residue TANGO aggregation score difference between the wild type protein and this variant. From left to right, all residue TANGO score differences from the N-terminus to the C-terminus are plotted. A flat line indicates that the variant does not alter the aggregation profile of the protein. Positive peaks indicate increased aggregation tendency due to this variant. Negative peaks indicate decreased aggregation tendency due to this variant.

Difference in TANGO aggregation between wild type and variant

This graph plots the per-residue TANGO aggregation score difference between the wild type protein and this variant.
From left to right, all residue TANGO score differences from the N-terminus to the C-terminus are plotted.
A flat line indicates that the variant does not alter the aggregation profile of the protein.
Positive peaks indicate increased aggregation tendency due to this variant.
Negative peaks indicate decreased aggregation tendency due to this variant.

TANGO aggregation profile score plot
	This graph plots the per-residue TANGO aggregation score of the variant protein. From left to right, all residue scores from the N-terminus to the C-terminus are plotted

Molecular visualization of TANGO aggregation-prone regions
Wild type 1B38_HUMAN	Variant VAR_016411
These two molecular images show the TANGO aggregation-prone regions as red colored segments. The left image represents the wild type protein, the right represents the variant protein. If both images are the same, it implies that the introduced variant amino acid does not alter the TANGO aggregation tendency. In any other case, the images allow structural interpretation of gained or lost aggregation-prone regions due to the variant amino acid. The structural location of the variant residue is colored in yellow. Click on the images to get a larger view and to download the original.

Molecular visualization of TANGO aggregation-prone regions

Wild type 1B38_HUMAN

Variant VAR_016411

These two molecular images show the TANGO aggregation-prone regions as red colored segments. The left image represents the wild type protein, the right represents the variant protein.
If both images are the same, it implies that the introduced variant amino acid does not alter the TANGO aggregation tendency. In any other case, the images allow structural interpretation of gained or lost aggregation-prone regions due to the variant amino acid.
The structural location of the variant residue is colored in yellow. Click on the images to get a larger view and to download the original.

WALTZ amylogenicity

Graphical comparison of WALTZ regions in variant and wild type
Protein	Predicted regions overview	WALTZ regions	Total score
Variant		2	866
Wild type		2	865

WALTZ regions in wild type and variant
Wild type WALTZ regions
N-term gatekeepers	WALTZ region	C-term gatekeepers	Start	End	Score
ENLRI	ALRYYN	QSEAG	105	110	48
LLRGH	NQFAYD	GKDYI	138	143	94
Variant protein WALTZ regions
N-term gatekeepers	WALTZ region	C-term gatekeepers	Start	End	Score
ENLRI	ALRYYN	QSEAG	105	110	48
LLRGH	NQFAYD	GKDYI	138	143	94

Difference in WALTZ amylogenicity between wild type and variant
	This graph plots the per-residue WALTZ amylogenic score difference between the wild type protein and this variant. From left to right, all residue WALTZ score differences from the N-terminus to the C-terminus are plotted. A flat line indicates that the variant does not alter the amylogenic profile of the protein. Positive peaks indicate increased amylogenic tendency due to this variant. Negative peaks indicate decreased amylogenic tendency due to this variant.

Difference in WALTZ amylogenicity between wild type and variant

This graph plots the per-residue WALTZ amylogenic score difference between the wild type protein and this variant.
From left to right, all residue WALTZ score differences from the N-terminus to the C-terminus are plotted.
A flat line indicates that the variant does not alter the amylogenic profile of the protein.
Positive peaks indicate increased amylogenic tendency due to this variant.
Negative peaks indicate decreased amylogenic tendency due to this variant.

WALTZ amylogenic profile score plot
	This graph plots the per-residue WALTZ amylogenic score of the variant protein. From left to right, all residue scores from the N-terminus to the C-terminus are plotted

Molecular visualization of WALTZ amylogenic regions
Wild type 1B38_HUMAN	Variant VAR_016411
These two molecular images show the WALTZ amylogenic regions as blue colored segments. The left image represents the wild type protein, the right represents the variant protein. If both images are the same, it implies that the introduced variant amino acid does not alter the WALTZ amyloid-forming tendency. In any other case, the images allow structural interpretation of gained or lost amylogenic regions due to the variant amino acid. The structural location of the variant residue is colored in yellow. Click on the images to get a larger view and to download the original.

Molecular visualization of WALTZ amylogenic regions

Wild type 1B38_HUMAN

Variant VAR_016411

These two molecular images show the WALTZ amylogenic regions as blue colored segments. The left image represents the wild type protein, the right represents the variant protein.
If both images are the same, it implies that the introduced variant amino acid does not alter the WALTZ amyloid-forming tendency. In any other case, the images allow structural interpretation of gained or lost amylogenic regions due to the variant amino acid.
The structural location of the variant residue is colored in yellow. Click on the images to get a larger view and to download the original.

LIMBO chaperone binding

Graphical comparison of LIMBO regions in variant and wild type
Protein	Predicted regions overview	LIMBO regions	Total score
Variant		5	3388
Wild type		5	3388

LIMBO regions in wild type and variant
Wild type LIMBO regions
N-term gatekeepers	WALTZ region	C-term gatekeepers	Start	End	Score
MAPRT	VLLLLSAA	LALTE	9	16	99
TYREN	LRIALRYYNQ	SEAGS	102	111	72
TCVEW	LRRYLENG	KETLQ	192	199	87
FYPAE	ITLTWQRD	GEDQT	237	244	46
GLPKP	LTLRWEPS	SQSTV	294	301	100
Variant protein LIMBO regions
N-term gatekeepers	WALTZ region	C-term gatekeepers	Start	End	Score
MAPRT	VLLLLSAA	LALTE	9	16	99
TYREN	LRIALRYYNQ	SEAGS	102	111	72
TCVEW	LRRYLENG	KETLQ	192	199	87
FYPAE	ITLTWQRD	GEDQT	237	244	46
GLPKP	LTLRWEPS	SQSTV	294	301	100

Difference in LIMBO chaperone binding between wild type and variant
	This graph plots the per-residue LIMBO chaperone binding difference between the wild type protein and this variant. From left to right, all residue LIMBO score differences from the N-terminus to the C-terminus are plotted. A flat line indicates that the variant does not alter the chaperone binding profile of the protein. Positive peaks indicate increased predicted chaperone binding due to this variant. Negative peaks indicate decreased predicted chaperone binding due to this variant.

Difference in LIMBO chaperone binding between wild type and variant

This graph plots the per-residue LIMBO chaperone binding difference between the wild type protein and this variant.
From left to right, all residue LIMBO score differences from the N-terminus to the C-terminus are plotted.
A flat line indicates that the variant does not alter the chaperone binding profile of the protein.
Positive peaks indicate increased predicted chaperone binding due to this variant.
Negative peaks indicate decreased predicted chaperone binding due to this variant.

LIMBO chaperone binding score plot
	This graph plots the per-residue LIMBO chaperone binding score of the variant protein. From left to right, all residue scores from the N-terminus to the C-terminus are plotted

Molecular visualization of LIMBO chaperone binding regions
Wild type 1B38_HUMAN	Variant VAR_016411
These two molecular images show the LIMBO chaperone binding regions as magenta colored segments. The left image represents the wild type protein, the right represents the variant protein. If both images are the same, it implies that the introduced variant amino acid does not alter the LIMBO chaperone binding properties. In any other case, the images allow structural interpretation of gained or lost chaperone binding regions due to the variant amino acid. The structural location of the variant residue is colored in yellow. Click on the images to get a larger view and to download the original.

Molecular visualization of LIMBO chaperone binding regions

Wild type 1B38_HUMAN

Variant VAR_016411

These two molecular images show the LIMBO chaperone binding regions as magenta colored segments. The left image represents the wild type protein, the right represents the variant protein.
If both images are the same, it implies that the introduced variant amino acid does not alter the LIMBO chaperone binding properties. In any other case, the images allow structural interpretation of gained or lost chaperone binding regions due to the variant amino acid.
The structural location of the variant residue is colored in yellow. Click on the images to get a larger view and to download the original.

FOLDX structural profile

There is currently no structural information available to make the required analyses.

Functional sites, structural features and cellular processing

Functional sites and structural features
Feature	This residue
Catalytic site	No
Secondary structure	No secondary structure information available
Transmembrane topology	outside

Cellular processing
Feature	Affected by variant
Signal peptide	No
Farnesylation anchor	No
N-Myristoylation anchor	No
Geranylgeranyl transferase Type 1 anchor	No
Geranylgeranyl transferase Type 2 anchor	No
Glycosylphosphatidylinositol (GPI) anchor	No
Peroxisomal targeting signal PTS1	No
Subcellular location	No

All mutations from 1B38_HUMAN

22 mutations listed

Variant	UniProt ID	Mutation	Disease	Mutation Type	dTANGO	dWALTZ	dLIMBO	ddG
VAR_061408	1B38_HUMAN	S48P	-	Polymorphism	-253	0	0	3.83
VAR_061407	1B38_HUMAN	S48A	-	Polymorphism	288	0	0	0.02
VAR_061409	1B38_HUMAN	S48T	-	Polymorphism	247	0	0	-0.46
VAR_056353	1B38_HUMAN	V306I	-	Polymorphism	0	0	0	N.A.
VAR_056354	1B38_HUMAN	A329T	-	Polymorphism	3	0	0	N.A.
VAR_059478	1B38_HUMAN	N87K	-	Polymorphism	2	0	1	-0.4
VAR_056350	1B38_HUMAN	V36M	-	Polymorphism	-8	0	0	-0.79
VAR_056352	1B38_HUMAN	N87D	-	Polymorphism	0	0	0	2.36
VAR_016418	1B38_HUMAN	N101S	-	Polymorphism	0	0	-14	0.35
VAR_016420	1B38_HUMAN	T187M	-	Polymorphism	0	0	0	-0.67
VAR_056348	1B38_HUMAN	V9L	-	Polymorphism	-16	0	0	N.A.
VAR_056349	1B38_HUMAN	L17V	-	Polymorphism	20	0	0	N.A.
VAR_056351	1B38_HUMAN	A65T	-	Polymorphism	0	0	0	0.13
VAR_016419	1B38_HUMAN	I104T	-	Polymorphism	0	1	-681	1.39
VAR_016417	1B38_HUMAN	Y98D	-	Polymorphism	0	-6	0	1.57
VAR_056347	1B38_HUMAN	M4T	-	Polymorphism	0	0	0	N.A.
VAR_016413	1B38_HUMAN	E82G	-	Polymorphism	0	0	0	2.2
VAR_016414	1B38_HUMAN	N87E	-	Polymorphism	0	0	0	1.09
VAR_016415	1B38_HUMAN	C91F	-	Polymorphism	0	6	0	-1.31
VAR_016416	1B38_HUMAN	C91S	-	Polymorphism	0	0	0	0.84
VAR_016412	1B38_HUMAN	E69T	-	Polymorphism	0	0	0	-0.59
VAR_016411	1B38_HUMAN	S35A	-	Polymorphism	53	1	0	-1.03