Variant VAR_004333 | SNPeffect 4.0

Phenotypic summary of VAR_004333

Compact overview of VAR_004333
UniProt ID	Gene	Mutation	Mutation type	Disease	OMIM	dbSNP
1A01_HUMAN	HLA-A	R41S	Polymorphism	-	No OMIM entry	No dbSNP entry

Short stretch summary of VAR_004333
Predictor	Predicted regions overview	Comparison to WT	Stretches in variant	Stretches in WT
Tango		-1 No change	6	6
Waltz		0 No change	0	0
Limbo		0 No change	5	5
Domain composition of 1A01_HUMAN
Database	Domain composition	Residue details
PFAM		MHC_I (Residues 25-203), C1-set (Residues 211-295), MHC_I_C (Residues 336-364)
SMART		IGc1 (Residues 222-293)

Structure stability summary of VAR_004333
Variant	Stability change	Effect	Structure	Stability frequency histogram
R41S	1.04 kcal/mol	Reduced stability

TANGO aggregation

Graphical comparison of TANGO regions in variant and wild type
Protein	Predicted regions overview	TANGO regions	Total score
Variant		6	2879
Wild type		6	2880

TANGO regions in wild type and variant
Wild type TANGO regions
N-term gatekeepers	TANGO region	C-term gatekeepers	Start	End	Score
VMAPR	TLLLLLSGALALT	QTWAG	8	20	44
HSMRY	FFTSV	SRPGR	32	36	6
RGEPR	FIAVGYV	DDTQF	46	52	77
FYPAE	ITLTW	QRDGE	237	241	13
GTFQK	WAAVV	VPSGE	268	272	11
QPTIP	IVGIIAGLVLLGAVITGAVVAAVMW	RRKSS	308	332	63
Variant protein TANGO regions
N-term gatekeepers	TANGO region	C-term gatekeepers	Start	End	Score
VMAPR	TLLLLLSGALALT	QTWAG	8	20	44
HSMRY	FFTSV	SRPGS	32	36	6
SGEPR	FIAVGYV	DDTQF	46	52	77
FYPAE	ITLTW	QRDGE	237	241	13
GTFQK	WAAVV	VPSGE	268	272	11
QPTIP	IVGIIAGLVLLGAVITGAVVAAVMW	RRKSS	308	332	63

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 1A01_HUMAN	Variant VAR_004333
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 1A01_HUMAN

Variant VAR_004333

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		0	21
Wild type		0	21

WALTZ regions in wild type and variant
Wild type WALTZ regions
N-term gatekeepers	WALTZ region	C-term gatekeepers	Start	End	Score
Variant protein WALTZ regions
N-term gatekeepers	WALTZ region	C-term gatekeepers	Start	End	Score

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 1A01_HUMAN	Variant VAR_004333
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 1A01_HUMAN

Variant VAR_004333

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	3190
Wild type		5	3190

LIMBO regions in wild type and variant
Wild type LIMBO regions
N-term gatekeepers	WALTZ region	C-term gatekeepers	Start	End	Score
MAPRT	LLLLLSGA	LALTQ	9	16	100
DGSHT	IQIMYGCD	VGPDG	119	126	11
IALNE	DLRSWTAA	DMAAQ	153	160	85
FYPAE	ITLTWQRD	GEDQT	237	244	100
GLPKP	LTLRWELS	SQPTI	294	301	97
Variant protein LIMBO regions
N-term gatekeepers	WALTZ region	C-term gatekeepers	Start	End	Score
MAPRT	LLLLLSGA	LALTQ	9	16	100
DGSHT	IQIMYGCD	VGPDG	119	126	11
IALNE	DLRSWTAA	DMAAQ	153	160	85
FYPAE	ITLTWQRD	GEDQT	237	244	100
GLPKP	LTLRWELS	SQPTI	294	301	97

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 1A01_HUMAN	Variant VAR_004333
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 1A01_HUMAN

Variant VAR_004333

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	TURN
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 1A01_HUMAN

16 mutations listed

Variant	UniProt ID	Mutation	Disease	Mutation Type	dTANGO	dWALTZ	dLIMBO	ddG
VAR_056253	1A01_HUMAN	R205H	-	Polymorphism	-1	0	0	1.35
VAR_056250	1A01_HUMAN	N151K	-	Polymorphism	0	0	0	0.24
VAR_056251	1A01_HUMAN	I166T	-	Polymorphism	0	0	0	0.96
VAR_056252	1A01_HUMAN	R169H	-	Polymorphism	-1	0	0	0.31
VAR_016725	1A01_HUMAN	V182A	-	Polymorphism	0	0	0	-0.31
VAR_056247	1A01_HUMAN	R89G	-	Polymorphism	-1	0	0	1.57
VAR_056248	1A01_HUMAN	G131W	-	Polymorphism	0	0	9	3.3
VAR_056249	1A01_HUMAN	F133L	-	Polymorphism	0	0	0	1.23
VAR_016723	1A01_HUMAN	I121M	-	Polymorphism	-11	-1	3	0.79
VAR_016724	1A01_HUMAN	R180L	-	Polymorphism	0	0	1	-1.91
VAR_016721	1A01_HUMAN	A100E	-	Polymorphism	0	0	0	-0.04
VAR_004333	1A01_HUMAN	R41S	-	Polymorphism	-1	0	0	1.04
VAR_016720	1A01_HUMAN	M91V	-	Polymorphism	0	0	0	4.3
VAR_016719	1A01_HUMAN	G80R	-	Polymorphism	1	0	0	0.47
VAR_004332	1A01_HUMAN	F33S	-	Polymorphism	-34	-6	0	6.14
VAR_016722	1A01_HUMAN	D114A	-	Polymorphism	0	0	0	0.42