UniProtKB/SwissProt variant VAR

Variant information

Variant position:

828

The position of the amino-acid change on the UniProtKB canonical protein sequence.

Type of variant:

LP/P [Disclaimer]

The variants are classified into three categories: LP/P, LB/B and US.

LP/P: likely pathogenic or pathogenic.
LB/B: likely benign or benign.
US: uncertain significance

Residue change:

From Tyrosine (Y) to Cysteine (C) at position 828 (Y828C, p.Tyr828Cys).

Indicates the amino acid change of the variant. The one-letter and three-letter codes for amino acids used in UniProtKB/Swiss-Prot are those adopted by the commission on Biochemical Nomenclature of the IUPAC-IUB.

Physico-chemical properties:

Change from large size and aromatic (Y) to medium size and polar (C)

The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:

-2

The score within a Blosum matrix for the corresponding wild-type to variant amino acid change. The log-odds score measures the logarithm for the ratio of the likelihood of two amino acids appearing by chance. The Blosum62 substitution matrix is used. This substitution matrix contains scores for all possible exchanges of one amino acid with another:

Lowest score: -4 (low probability of substitution).
Highest score: 11 (high probability of substitution).

More information can be found on the following page

Variant description:

In FHCL1; J.D.Bari/Syria; 2-fold decreased affinity for LDLRAP1.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs28942085 [ dbSNP | Ensembl ]

Sequence information

Variant position:

828

The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:

860

The length of the canonical sequence.

Location on the sequence:

LLWKNWRLKNINSINFDNPV Y QKTTEDEVHICHNQDGYSYP

The residue change on the sequence. Unless the variant is located at the beginning or at the end of the protein sequence, both residues upstream (20) and downstream (20) of the variant will be shown.

Residue conservation:

The multiple alignment of the region surrounding the variant against various orthologous sequences.

Human                         LLWKNWRLKNINSINFDNPVYQKTTEDEVHICHNQDGYSYP

Mouse                         LLWRNWRLKNINSINFDNPVYQKTTEDELHICRSQDGYTYP

Rat                           LLWRNWRLRNINSINFDNPVYQKTTEDEIHICRSQDGYTYP

Bovine                        LLWKNWRLKSINSINFDNPVYQKTTEDEVHICRSQDGYTYP

Sequence annotation in neighborhood:

The regions or sites of interest surrounding the variant. In general the features listed are posttranslational modifications, binding sites, enzyme active sites, local secondary structure or other characteristics reported in the cited references. The "Sequence annotation in neighborhood" lines have a fixed format:

Type: the type of sequence feature.
Positions: endpoints of the sequence feature.
Description: contains additional information about the feature.

Type	Positions	Description
Chain	22 – 860	Low-density lipoprotein receptor
Topological domain	811 – 860	Cytoplasmic
Region	811 – 860	Required for MYLIP-triggered down-regulation of LDLR
Motif	823 – 828	NPXY motif
Mutagenesis	811 – 811	K -> R. No change. No change; when associated with R-816 and R-830. Insensitive to MYLIP-triggered degradation; when associated with R-816; R-830 and A-839.
Mutagenesis	816 – 816	K -> R. No change. No change; when associated with R-830. No change; when associated with R-811 and R-830. Insensitive to MYLIP-triggered degradation; when associated with R-830 and A-839. Insensitive to MYLIP-triggered degradation; when associated with R-811; R-830 and A-839.
Mutagenesis	821 – 821	I -> A. 3-fold decreased affinity for LDLRAP1.
Mutagenesis	821 – 821	I -> R. 10-fold decreased affinity for LDLRAP1.
Mutagenesis	828 – 828	Y -> A. Abolishes interaction with ARRB2.
Mutagenesis	829 – 829	Q -> A. Decreased affinity for LDLRAP1.
Mutagenesis	830 – 830	K -> R. No change. No change; when associated with R-816. No change; when associated with R-811 and R-816. Insensitive to MYLIP-triggered degradation; when associated with A-839. Insensitive to MYLIP-triggered degradation; when associated with R-816 and A-839. Insensitive to MYLIP-triggered degradation; when associated with R-811; R-816 and A-839.
Mutagenesis	839 – 839	C -> A. No change. Insensitive to MYLIP-triggered degradation; when associated with R-830. Insensitive to MYLIP-triggered degradation; when associated with R-816 and R-830. Insensitive to MYLIP-triggered degradation; when associated with R-811; R-816 and R-830.
Turn	826 – 829

Literature citations

Atomic structure of the autosomal recessive hypercholesterolemia phosphotyrosine-binding domain in complex with the LDL-receptor tail.
Dvir H.; Shah M.; Girardi E.; Guo L.; Farquhar M.G.; Zajonc D.M.;
Proc. Natl. Acad. Sci. U.S.A. 109:6916-6921(2012)
Cited for: X-RAY CRYSTALLOGRAPHY (1.37 ANGSTROMS) OF 819-832 IN COMPLEX WITH LDLRAP1; INTERACTION WITH LDLRAP1; CHARACTERIZATION OF VARIANT FHCL1 CYS-828; MUTAGENESIS OF ILE-821 AND GLN-829; TOPOLOGY; MOTIF;

The J.D. mutation in familial hypercholesterolemia: amino acid substitution in cytoplasmic domain impedes internalization of LDL receptors.
Davis C.G.; Lehrman M.A.; Russell D.W.; Anderson R.G.W.; Brown M.S.; Goldstein J.L.;
Cell 45:15-24(1986)
Cited for: VARIANT FHCL1 CYS-828;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P01130: Variant p.Tyr828Cys