Variant information:

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Variant position: 84

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

Type of variant: Polymorphism

The variants are classified into three categories: Disease, Polymorphism and Unclassified.

• Disease: Variants have been found in patients and disease-association is reported in literature. However, this classification is not a definitive assessment of variant pathogenicity.
• Polymorphism: No disease-association has been reported.
• Unclassified: Variants have been found in patients but disease-association remains unclear.

Residue change: From Proline (P) to Leucine (L) at position 84 (P84L, p.Pro84Leu).

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 hydrophobic.

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

BLOSUM score: -3

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: Genetic variations in TNF influence susceptibility to hepatitis B virus (HBV) infection [MIM:610424].Genetic variations in TNF are involved in susceptibility to malaria [MIM:611162]. -

Additional information on the polymorphism described.

Other resources: 

Links to websites of interest for the variant.

• Wikipedia; Tumor necrosis factor alpha entry
• Atlas of Genetics and Cytogenetics in Oncology and Haematology
• NIEHS-SNPs
• SeattleSNPs
• SHMPD; The Singapore human mutation and polymorphism database
• Variant rs4645843 [ dbSNP | Ensembl ]

Sequence information:

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Variant position: 84

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

Protein sequence length: 233

The length of the canonical sequence.

Location on the sequence:  PRDLSLISPLAQAVRSSSRT  P SDKPVAHVVANPQAEGQLQW

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                         PRDLSLISPLAQ--AVRSSSRTPSDKPVAHVVANPQAEGQLQW

Rhesus macaque                PKDPSLISPLAQ--AVRSSSRTPSDKPVAHVVANPQAEGQL

Chimpanzee                    PRDLSLISPLAQ---AGSSSRTPSDKPVAHVVANPQAEGQL

Mouse                         PNGLPLISSMAQTLTLRSSSQNSSDKPVAHVVANHQVEEQL

Rat                           PNGLPLISSMAQTLTLRSSSQNSSDKPVAHVVANHQAEEQL

Pig                           PAGPLSINPLAQ--GLRSSSQT-SDKPVAHVVANVKAEGQL

Bovine                        PGGPSINSPLVQ--TLRSSSQASSNKPVAHVVADINSPGQL

Rabbit                        PNNLHLVNPVAQMVTLRSASRALSDKPLAHVVANPQVEGQL

Goat                          PAGPSFNRPLVQ--TLRSSSQASSNKPVAHVVANISAPGQL

Sheep                         PAGPSFNRPLVQ--TLRSSSQASNNKPVAHVVANISAPGQL

Cat                           PHGLQLINPLPQ--TLRSSSRTPSDKPVAHVVANPEAEGQL

Dog                           PNGLQLISPLAQ--TVKSSSRTPSDKPVAHVVANPEAEGQL

Horse                         PNAFQSINPLAQ--TLRSSSRTPSDKPVAHVVANPQAEGQL

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 – 233	Tumor necrosis factor, membrane form
Chain	77 – 233	Tumor necrosis factor, soluble form
Topological domain	57 – 233	Extracellular
Glycosylation	80 – 80	O-linked (GalNAc...); in soluble form

Literature citations

Submission
NIEHS SNPs program;
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]; VARIANT LEU-84;