UniProtKB/SwissProt variant VAR

Variant information

Variant position:

114

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 114 (R114C, p.Arg114Cys).

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 IMD28; encodes misfolded protein with abnormal glycosylation; affects receptor trafficking to the cell surface; reduces response to IFNG.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs1243506079 [ dbSNP | Ensembl ]

Sequence information

Variant position:

114

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

Protein sequence length:

337

The length of the canonical sequence.

Location on the sequence:

CDFTAASPSAGFPMDFNVTL R LRAELGALHSAWVTMPWFQH

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.

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 – 337	Interferon gamma receptor 2
Topological domain	28 – 247	Extracellular
Domain	31 – 129	Fibronectin type-III 1
Glycosylation	110 – 110	N-linked (GlcNAc...) asparagine
Mutagenesis	110 – 110	N -> Q. Complete inhibition of transport to the cell membrane.
Beta strand	109 – 119

Literature citations

Partial interferon-gamma receptor signaling chain deficiency in a patient with bacille Calmette-Guerin and Mycobacterium abscessus infection.
Doeffinger R.; Jouanguy E.; Dupuis S.; Fondaneche M.C.; Stephan J.L.; Emile J.F.; Lamhamedi-Cherradi S.; Altare F.; Pallier A.; Barcenas-Morales G.; Meinl E.; Krause C.; Pestka S.; Schreiber R.D.; Novelli F.; Casanova J.L.;
J. Infect. Dis. 181:379-384(2000)
Cited for: VARIANT IMD28 CYS-114;

Partial IFN-gammaR2 deficiency is due to protein misfolding and can be rescued by inhibitors of glycosylation.
Moncada-Velez M.; Martinez-Barricarte R.; Bogunovic D.; Kong X.F.; Blancas-Galicia L.; Tirpan C.; Aksu G.; Vincent Q.B.; Boisson B.; Itan Y.; Ramirez-Alejo N.; Okada S.; Kreins A.Y.; Bryant V.L.; Franco J.L.; Migaud M.; Espinosa-Padilla S.; Yamazaki-Nakashimada M.; Espinosa-Rosales F.; Kutukculer N.; Abel L.; Bustamante J.; Vogt G.; Casanova J.L.; Boisson-Dupuis S.;
Blood 122:2390-2401(2013)
Cited for: VARIANTS IMD28 PHE-124 AND ARG-141; CHARACTERIZATION OF VARIANTS IMD28 CYS-114; PHE-124; ARG-141; ASN-168 AND ARG-227; SUBCELLULAR LOCATION;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P38484: Variant p.Arg114Cys