Home  |  Contact

UniProtKB/Swiss-Prot Q8TDQ0: Variant p.Tyr82Cys

Hepatitis A virus cellular receptor 2
Gene: HAVCR2
Variant information

Variant position:  82
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Type of variant:  Disease [Disclaimer]
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 82 (Y82C, p.Tyr82Cys).
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

Involvement in disease:  T-cell lymphoma, subcutaneous panniculitis-like (SPTCL) [MIM:618398]: An uncommon form of T-cell non-Hodgkin lymphoma, in which cytotoxic CD8+ T-cells infiltrate subcutaneous adipose tissue, and rimming adipocytes in a lace-like pattern. Affected individuals typically present with multiple subcutaneous nodules, systemic B-cell symptoms, and, in a subset of cases, autoimmune disorders, most commonly systemic lupus erythematosus. A subset of patients develop hemophagocytic lymphohistiocytosis. SPTCL transmission pattern is consistent with autosomal recessive inheritance with incomplete penetrance. {ECO:0000269|PubMed:30374066, ECO:0000269|PubMed:30792187, ECO:0000269|Ref.2}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.
The name and a short description of the disease associated with the variant. For more information about the disease, the user can refer to OMIM, following the link provided after the disease acronym.

Variant description:  In SPTCL; associated with disease susceptibility; results in dysregulated secretion of inflammatory cytokines by macrophages; affects protein folding; decreased localization at the cell membrane.
Any additional useful information about the variant.

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



Sequence information

Variant position:  82
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  301
The length of the canonical sequence.

Location on the sequence:   ECGNVVLRTDERDVNYWTSR  Y WLNGDFRKGDVSLTIENVTL
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                         ECGNVVLRTDERDVNY-WTSRYWLNGDFRKGDVSLTIENVTL

Mouse                         QCTNELLRTDERNVTYQKSSRYQLKGDLNKGDVSLIIKNVT

Rat                           QCASVVLRTDETNVTYRKSRRYQLKGNFYKGDMSLTIKNVT

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 22 – 301 Hepatitis A virus cellular receptor 2
Topological domain 22 – 202 Extracellular
Domain 22 – 124 Ig-like V-type
Disulfide bond 38 – 110
Disulfide bond 58 – 109
Beta strand 82 – 86


Literature citations

Germline HAVCR2 mutations altering TIM-3 characterize subcutaneous panniculitis-like T cell lymphomas with hemophagocytic lymphohistiocytic syndrome.
Gayden T.; Sepulveda F.E.; Khuong-Quang D.A.; Pratt J.; Valera E.T.; Garrigue A.; Kelso S.; Sicheri F.; Mikael L.G.; Hamel N.; Bajic A.; Dali R.; Deshmukh S.; Dervovic D.; Schramek D.; Guerin F.; Taipale M.; Nikbakht H.; Majewski J.; Moshous D.; Charlebois J.; Abish S.; Bole-Feysot C.; Nitschke P.; Bader-Meunier B.; Mitchell D.; Thieblemont C.; Battistella M.; Gravel S.; Nguyen V.H.; Conyers R.; Diana J.S.; McCormack C.; Prince H.M.; Besnard M.; Blanche S.; Ekert P.G.; Fraitag S.; Foulkes W.D.; Fischer A.; Neven B.; Michonneau D.; de Saint Basile G.; Jabado N.;
Nat. Genet. 50:1650-1657(2018)
Cited for: INVOLVEMENT IN SPTCL; SUBCELLULAR LOCATION; VARIANTS SPTCL CYS-82 AND MET-97; CHARACTERIZATION OF VARIANTS SPTCL CYS-82 AND MET-97;

Frequent germline mutations of HAVCR2 in sporadic subcutaneous panniculitis-like T-cell lymphoma.
Polprasert C.; Takeuchi Y.; Kakiuchi N.; Yoshida K.; Assanasen T.; Sitthi W.; Bunworasate U.; Pirunsarn A.; Wudhikarn K.; Lawasut P.; Uaprasert N.; Kongkiatkamon S.; Moonla C.; Sanada M.; Akita N.; Takeda J.; Fujii Y.; Suzuki H.; Nannya Y.; Shiraishi Y.; Chiba K.; Tanaka H.; Miyano S.; Rojnuckarin P.; Ogawa S.; Makishima H.;
Blood Adv. 3:588-595(2019)
Cited for: INVOLVEMENT IN SPTCL; VARIANTS SPTCL CYS-82 AND ILE-101;

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.