UniProtKB/Swiss-Prot Q06643: Variant p.Ala122Asp

Lymphotoxin-beta
Gene: LTB
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Variant information Variant position:

122 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Type of variant:

LB/B 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 Alanine (A) to Aspartate (D) at position 122 (A122D, p.Ala122Asp). 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 small size and hydrophobic (A) to medium size and acidic (D) 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
Other resources:

Links to websites of interest for the variant.

Variant rs2229699 [ dbSNP | Ensembl ]

Sequence information Variant position:

122 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length:

244 The length of the canonical sequence.
Location on the sequence:

LGWETTKEQAFLTSGTQFSD A EGLALPQDGLYYLYCLVGYR 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                         LGWETTKEQAFLTSGTQFSDAEGLALPQDGLYYLYCLVGYR

Rhesus macaque                LGWEATKEQAFLTSGTQFSDADGLALPQDGLYYLYCLVGYR

Chimpanzee                    LGWETTKEQAFLTSGTQFSDAEGLALPQDGLYYLYCLVGYR

Mouse                         LSWEASQEEAFLRSGAQFSPTHGLALPQDGVYYLYCHVGYR

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	1 – 244	Lymphotoxin-beta
Topological domain	49 – 244	Extracellular
Domain	88 – 243	THD
Alternative sequence	78 – 244	Missing. In isoform 2.
Mutagenesis	108 – 108	K -> E. In subunit 1; reduces binding of LTA(1)-LTB(2) to LTBR and abolishes LTBR-mediated NF-kappa-B signaling activation; when associated with R-109 and E-142, and 'A-142' in LTA. In subunit 2; reduces binding of LTA(1)-LTB(2) to LTBR and abolishes LTBR-mediated NF-kappa-B signaling activation; when associated with R-109 and E-142, and with 'A-170' in LTB (subunit 1). In subunit 1; abolishes binding of LTA(1)-LTB(2) to LTBR and abolishes LTBR-mediated NF-kappa-B signaling activation; when associated with R-109; E-142 and A-170, and with 'E-108'; 'R-109' and 'E-142' in LTB (subunit 2), and with 'A-142' in LTA.
Mutagenesis	109 – 109	E -> R. In subunit 1; reduces binding of LTA(1)-LTB(2) to LTBR and abolishes LTBR-mediated NF-kappa-B signaling activation; when associated with E-108 and E-142, and 'A-142' in LTA. In subunit 2; reduces binding of LTA(1)-LTB(2) to LTBR and abolishes LTBR-mediated NF-kappa-B signaling activation; when associated with E-108 and E-142, and with 'A-170' in LTB (subunit 1). In subunit 1; abolishes binding of LTA(1)-LTB(2) to LTBR and abolishes LTBR-mediated NF-kappa-B signaling activation; when associated with E-108; E-142 and A-170, and with 'E-108'; 'R-109' and 'E-142' in LTB (subunit 2), and with 'A-142' in LTA.
Mutagenesis	142 – 142	R -> E. In subunit 1; reduces binding of LTA(1)-LTB(2) to LTBR and abolishes LTBR-mediated NF-kappa-B signaling activation; when associated with E-108 and R-109, and 'A-142' in LTA. In subunit 2; reduces binding of LTA(1)-LTB(2) to LTBR and abolishes LTBR-mediated NF-kappa-B signaling activation; when associated with E-108 and R-109, and with 'A-170' in LTB (subunit 1). In subunit 1; abolishes binding of LTA(1)-LTB(2) to LTBR and abolishes LTBR-mediated NF-kappa-B signaling activation; when associated with E-108; R-109 and A-170, and with 'E-108'; 'R-109' and 'E-142' in LTB (subunit 2), and with 'A-142' in LTA.

Literature citations
No reference for the current variant in UniProtKB/Swiss-Prot.

Disclaimer: Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. They are not in any way intended to be used as a substitute for professional medical advice, diagnostic, treatment or care.