UniProtKB/SwissProt variant VAR

Variant information

Variant position:

129

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 Arginine (R) to Cysteine (C) at position 129 (R129C, p.Arg129Cys).

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 basic (R) to medium size and polar (C)

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

Variant description:

In OPTB7; a patient with osteoclast-poor osteopetrosis.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs121908657 [ dbSNP | Ensembl ]

Sequence information

Variant position:

129

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

Protein sequence length:

616

The length of the canonical sequence.

Location on the sequence:

PRRCACTAGYHWSQDCECCR R NTECAPGLGAQHPLQLNKDT

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                         PRRCACTAGYHWSQDCECCRRNTECAPGLGAQHPLQLNKDT

Mouse                         PRRCACTAGYHWNSDCECCRRNTECAPGFGAQHPLQLNKDT

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	30 – 616	Tumor necrosis factor receptor superfamily member 11A
Topological domain	30 – 212	Extracellular
Repeat	114 – 151	TNFR-Cys 3
Metal binding	133 – 133	Sodium; via carbonyl oxygen
Metal binding	134 – 134	Sodium; via carbonyl oxygen

Literature citations

Human osteoclast-poor osteopetrosis with hypogammaglobulinemia due to TNFRSF11A (RANK) mutations.
Guerrini M.M.; Sobacchi C.; Cassani B.; Abinun M.; Kilic S.S.; Pangrazio A.; Moratto D.; Mazzolari E.; Clayton-Smith J.; Orchard P.; Coxon F.P.; Helfrich M.H.; Crockett J.C.; Mellis D.; Vellodi A.; Tezcan I.; Notarangelo L.D.; Rogers M.J.; Vezzoni P.; Villa A.; Frattini A.;
Am. J. Hum. Genet. 83:64-76(2008)
Cited for: VARIANTS OPTB7 ARG-53; CYS-129; GLY-170; ARG-175 AND SER-244;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q9Y6Q6: Variant p.Arg129Cys