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UniProtKB/Swiss-Prot P15260: Variant p.Tyr397Cys

Interferon gamma receptor 1
Gene: IFNGR1
Chromosomal location: 6q23-q24
Variant information

Variant position:  397
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 implicated in disease according to literature reports.
  • Polymorphism: Variants not reported to be implicated in disease.
  • Unclassified: Variants with uncertain implication in disease according to literature reports. Evidence against or in favor of a pathogenic role is limited and/or conflicting.

Residue change:  From Tyrosine (Y) to Cysteine (C) at position 397 (Y397C, p.Tyr397Cys).
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 aromatic (Y) to medium size and polar (C)
The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:  -2
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 genetic variation in the IFNGR1 gene is associated with susceptibility to Helicobacter pylori infection [MIM:600263].
Additional information on the polymorphism described.

Variant description:  Functional polymorphism; associated with susceptibility to atopic dermatitis complicated by eczema herpeticum; does not affect completely interferon-gamma-mediated signaling pathway.
Any additional useful information about the variant.

Other resources:  
Links to websites of interest for the variant.



Sequence information

Variant position:  397
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  489
The length of the canonical sequence.

Location on the sequence:   ESSSPLSSNQSEPGSIALNS  Y HSRNCSESDHSRNGFDTDSS
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                         ESSSPLSSNQSEPGSIALNSYHSRNCSESDHSRNGFDTDSS

Mouse                         RSFSLLSSNQSGPCS--LTAYHSRNGS-----------DSG

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.

TypePositionsDescription
Chain 18 – 489 Interferon gamma receptor 1
Topological domain 267 – 489 Cytoplasmic
Modified residue 378 – 378 Phosphoserine
Modified residue 403 – 403 Phosphoserine
Alternative sequence 197 – 489 Missing. In isoform 2.


Literature citations

Targeted deep sequencing identifies rare loss-of-function variants in IFNGR1 for risk of atopic dermatitis complicated by eczema herpeticum.
Gao L.; Bin L.; Rafaels N.M.; Huang L.; Potee J.; Ruczinski I.; Beaty T.H.; Paller A.S.; Schneider L.C.; Gallo R.; Hanifin J.M.; Beck L.A.; Geha R.S.; Mathias R.A.; Barnes K.C.; Leung D.Y.M.;
J. Allergy Clin. Immunol. 136:1591-1600(2015)
Cited for: CHARACTERIZATION OF VARIANTS MET-14; ILE-61 AND CYS-397;

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.