Variant VAR_004335 | SNPeffect 4.0

Phenotypic summary of VAR_004335

Compact overview of VAR_004335
UniProt ID	Gene	Mutation	Mutation type	Disease	OMIM	dbSNP
1A02_HUMAN	HLA-A	D54N	Polymorphism	-	No OMIM entry	No dbSNP entry

Short stretch summary of VAR_004335
Predictor	Predicted regions overview	Comparison to WT	Stretches in variant	Stretches in WT
Tango		81 Increased	6	6
Waltz		0 No change	2	2
Limbo		0 No change	5	5
Domain composition of 1A02_HUMAN
Database	Domain composition	Residue details
PFAM		MHC_I (Residues 25-203), C1-set (Residues 212-295), MHC_I_C (Residues 336-364)
SMART		IGc1 (Residues 222-293)

Structure stability summary of VAR_004335
Variant	Stability change	Effect	Structure	Stability frequency histogram
D54N	-0.32 kcal/mol	No effect on stability

TANGO aggregation

Graphical comparison of TANGO regions in variant and wild type
Protein	Predicted regions overview	TANGO regions	Total score
Variant		6	3036
Wild type		6	2956

TANGO regions in wild type and variant
Wild type TANGO regions
N-term gatekeepers	TANGO region	C-term gatekeepers	Start	End	Score
VMAPR	TLVLLLSGALALT	QTWAG	8	20	51
HSMRY	FFTSV	SRPGR	32	36	6
RGEPR	FIAVGYV	DDTQF	46	52	77
FYPAE	ITLTW	QRDGE	237	241	13
GTFQK	WAAVV	VPSGQ	268	272	11
QPTIP	IVGIIAGLVLFGAVITGAVVAAVMW	RRKSS	308	332	63
Variant protein TANGO regions
N-term gatekeepers	TANGO region	C-term gatekeepers	Start	End	Score
VMAPR	TLVLLLSGALALT	QTWAG	8	20	51
HSMRY	FFTSV	SRPGR	32	36	6
RGEPR	FIAVGYV	DNTQF	46	52	89
FYPAE	ITLTW	QRDGE	237	241	13
GTFQK	WAAVV	VPSGQ	268	272	11
QPTIP	IVGIIAGLVLFGAVITGAVVAAVMW	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 1A02_HUMAN	Variant VAR_004335
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 1A02_HUMAN

Variant VAR_004335

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	186
Wild type		2	187

WALTZ regions in wild type and variant
Wild type WALTZ regions
N-term gatekeepers	WALTZ region	C-term gatekeepers	Start	End	Score
FLRGY	HQYAYD	GKDYI	138	143	22
TLRCW	ALSFYP	AEITL	229	234	6
Variant protein WALTZ regions
N-term gatekeepers	WALTZ region	C-term gatekeepers	Start	End	Score
FLRGY	HQYAYD	GKDYI	138	143	22
TLRCW	ALSFYP	AEITL	229	234	6

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 1A02_HUMAN	Variant VAR_004335
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 1A02_HUMAN

Variant VAR_004335

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	3189
Wild type		5	3189

LIMBO regions in wild type and variant
Wild type LIMBO regions
N-term gatekeepers	WALTZ region	C-term gatekeepers	Start	End	Score
MAPRT	LVLLLSGA	LALTQ	9	16	100
VGSDW	RFLRGYHQ	YAYDG	132	139	66
TCVEW	LRRYLENG	KETLQ	192	199	87
FYPAE	ITLTWQRD	GEDQT	237	244	46
GLPKP	LTLRWEPS	SQPTI	294	301	98
Variant protein LIMBO regions
N-term gatekeepers	WALTZ region	C-term gatekeepers	Start	End	Score
MAPRT	LVLLLSGA	LALTQ	9	16	100
VGSDW	RFLRGYHQ	YAYDG	132	139	66
TCVEW	LRRYLENG	KETLQ	192	199	87
FYPAE	ITLTWQRD	GEDQT	237	244	46
GLPKP	LTLRWEPS	SQPTI	294	301	98

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 1A02_HUMAN	Variant VAR_004335
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 1A02_HUMAN

Variant VAR_004335

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 1A02_HUMAN

22 mutations listed

Variant	UniProt ID	Mutation	Disease	Mutation Type	dTANGO	dWALTZ	dLIMBO	ddG
VAR_016730	1A02_HUMAN	W191G	-	Polymorphism	0	-1	8	1.99
VAR_004350	1A02_HUMAN	A260E	-	Polymorphism	0	0	0	1.31
VAR_004349	1A02_HUMAN	T187E	-	Polymorphism	0	-1	0	-1.03
VAR_016728	1A02_HUMAN	H98D	-	Polymorphism	0	0	0	1.96
VAR_016729	1A02_HUMAN	E190D	-	Polymorphism	0	-1	0	0.41
VAR_004348	1A02_HUMAN	L180Q	-	Polymorphism	0	1	0	1.75
VAR_016727	1A02_HUMAN	H94Q	-	Polymorphism	0	0	0	-0.31
VAR_016726	1A02_HUMAN	A65G	-	Polymorphism	0	0	0	0.23
VAR_004344	1A02_HUMAN	M162K	-	Polymorphism	1	0	0	-0.28
VAR_004347	1A02_HUMAN	L180W	-	Polymorphism	0	-1	0	-0.56
VAR_004345	1A02_HUMAN	A173T	-	Polymorphism	0	0	0	0.3
VAR_004346	1A02_HUMAN	V176E	-	Polymorphism	0	0	0	0.69
VAR_004337	1A02_HUMAN	K90N	-	Polymorphism	-1	0	0	-0.06
VAR_004343	1A02_HUMAN	W131G	-	Polymorphism	0	-1	-529	-0.56
VAR_004338	1A02_HUMAN	T97I	-	Polymorphism	0	0	0	-0.54
VAR_004339	1A02_HUMAN	V119L	-	Polymorphism	0	0	0	-0.63
VAR_004340	1A02_HUMAN	R121M	-	Polymorphism	0	0	1	0.57
VAR_004341	1A02_HUMAN	Y123C	-	Polymorphism	0	0	0	2.15
VAR_004342	1A02_HUMAN	Y123F	-	Polymorphism	0	0	0	0.22
VAR_004335	1A02_HUMAN	D54N	-	Polymorphism	81	0	0	-0.32
VAR_004336	1A02_HUMAN	Q67R	-	Polymorphism	1	0	786	0.48
VAR_004334	1A02_HUMAN	F33Y	-	Polymorphism	-24	-3	0	0.92