UniProtKB/Swiss-Prot Q07011: Variant p.Gly109Ser

Tumor necrosis factor receptor superfamily member 9
Gene: TNFRSF9
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Variant information Variant position:

109 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Type of variant:

US 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 Glycine (G) to Serine (S) at position 109 (G109S, p.Gly109Ser). 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 glycine (G) to small size and polar (S) The physico-chemical property of the reference and variant residues and the change implicated.
BLOSUM score:

0 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 IMD109; uncertain significance; contrary to wild-type, undetectable in patient's stimulated peripheral blood mononuclear cells; patient's cells show defective expansion, reduced expression of IFNG and perforin/PRF1 and impaired allospecific and EBV-specific cytotoxic activity, as well as reduced mitochondrial function. Any additional useful information about the variant.

Sequence information Variant position:

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

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

TPGFHCLGAGCSMCEQDCKQ G QELTKKGCKDCCFGTFNDQK 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                         TPGFHCLGAGCSMCEQDCKQGQELTKKGCKDCCFGTFNDQK-

Mouse                         IEGFHCLGPQCTRCEKDCRPGQELTKQGCKTCSLGTFNDQN

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	24 – 255	Tumor necrosis factor receptor superfamily member 9
Topological domain	24 – 186	Extracellular
Repeat	87 – 118	TNFR-Cys 3
Disulfide bond	102 – 117

Literature citations
Immunodeficiency and EBV-induced lymphoproliferation caused by 4-1BB deficiency.
Alosaimi M.F.; Hoenig M.; Jaber F.; Platt C.D.; Jones J.; Wallace J.; Debatin K.M.; Schulz A.; Jacobsen E.; Moeller P.; Shamseldin H.E.; Abdulwahab F.; Ibrahim N.; Alardati H.; Almuhizi F.; Abosoudah I.F.; Basha T.A.; Chou J.; Alkuraya F.S.; Geha R.S.;
J. Allergy Clin. Immunol. 144:574-583(2019)
Cited for: INVOLVEMENT IN IMD109; VARIANT IMD109 SER-109; CHARACTERIZATION OF VARIANT IMD109 SER-109; FUNCTION; TISSUE SPECIFICITY;

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.