UniProtKB/Swiss-Prot O00300: Variant p.Val104Met

Tumor necrosis factor receptor superfamily member 11B
Gene: TNFRSF11B
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Variant information Variant position:

104 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 Valine (V) to Methionine (M) at position 104 (V104M, p.Val104Met). 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:

1 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 rs11573906 [ dbSNP | Ensembl ]

Sequence information Variant position:

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

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

SPVCKELQYVKQECNRTHNR V CECKEGRYLEIEFCLKHRSC 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                         SPVCKELQYVKQECNRTHNRVCECKEGRYLEIEFCLKHRSC

Mouse                         SPVCKELQSVKQECNRTHNRVCECEEGRYLEIEFCLKHRSC

Rat                           SPVCKELQTVKQECNRTHNRVCECEEGRYLELEFCLKHRSC

Bovine                        SPVCKELQYVKQECSRTHNRVCECEEGRYLELEFCLKHRSC

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 – 401	Tumor necrosis factor receptor superfamily member 11B
Repeat	65 – 105	TNFR-Cys 2
Glycosylation	98 – 98	N-linked (GlcNAc...) asparagine
Disulfide bond	87 – 105
Mutagenesis	116 – 116	E -> A. Reduces affinity for TNFSF11. Decreases inhibition of osteoclast differentiation.
Beta strand	104 – 107

Literature citations
Submission
NIEHS SNPs program;
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]; VARIANTS LYS-3 AND MET-104;

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.