UniProtKB/Swiss-Prot P01374: Variant p.Thr60Asn

Lymphotoxin-alpha
Gene: LTA
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Variant information Variant position:

60 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 Threonine (T) to Asparagine (N) at position 60 (T60N, p.Thr60Asn). 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:

Similar physico-chemical property. Both residues are medium size and polar. The physico-chemical property of the reference and variant residues and the change implicated.
BLOSUM score:

0 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
Polymorphism:

A polymorphism in LTA accounts, in part, for susceptibility to leprosy linked to chromosome 6p21.3 (LPRS4) [MIM:610988]. Additional information on the polymorphism described.
Variant description:

In allele TNFB*2. Any additional useful information about the variant.
Other resources:

Links to websites of interest for the variant.

Variant rs1041981 [ dbSNP | Ensembl ]

Sequence information Variant position:

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

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

LTPSAAQTARQHPKMHLAHS T LKPAAHLIGDPSKQNSLLWR 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                         LTPSAAQTARQHPKMHLAHSTLKPAAHLIGDPSKQNSLLWR

                              ISPSAARTAYQHPQKHFIQGTLKPAAHLIGDPSIQNSLRWR

Rhesus macaque                LTPSAAQTARQHPKMHLAHSTLKPAAHLIGDPSKQNSLLWR

Chimpanzee                    LTPSAAQTARQHPKMHLAHSTLKPAAHLIGDPSKQNSLLWR

Mouse                         F--SAARTAHPLPQKHLTHGILKPAAHLVGYPSKQNSLLWR

Rat                           F--SASRTAHQPPQKHLTHGLLKPAAHLVGYPSKQNSLLWR

Pig                           LPPSAAQPAHQHPPKHLARGTLKPAAHLVGDPSTPDSLRWR

Bovine                        LTPSAAQPAHQQLPTPFTRGTLKPAAHLVGDPSTQDSLRWR

Rabbit                        FPPSAARNAQQRLQKHFGHSTLKPAAHLVGDPSAQDSLRWR

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	35 – 205	Lymphotoxin-alpha
Glycosylation	41 – 41	O-linked (GalNAc...) threonine; partial

Literature citations
Submission
SeattleSNPs variation discovery resource;
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]; VARIANTS ARG-13; PRO-51 AND ASN-60; Submission
NIEHS SNPs program;
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]; VARIANTS ARG-13; PRO-51 AND ASN-60; Natural human tumor necrosis factor beta (lymphotoxin). Variable O-glycosylation at Thr7, proteolytic processing, and allelic variation.
Voigt C.G.; Maurer-Fogy I.; Adolf G.R.;
FEBS Lett. 314:85-88(1992)
Cited for: PARTIAL PROTEIN SEQUENCE; GLYCOSYLATION AT THR-41 AND ASN-96; VARIANT ASN-60; Polymorphic structure of the tumor necrosis factor (TNF) locus: an NcoI polymorphism in the first intron of the human TNF-beta gene correlates with a variant amino acid in position 26 and a reduced level of TNF-beta production.
Messer G.; Spengler U.; Jung M.C.; Honold G.; Bloemer K.; Pape G.R.; Riethmueller G.; Weiss E.H.;
J. Exp. Med. 173:209-219(1991)
Cited for: VARIANT ASN-60;

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.