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UniProtKB/Swiss-Prot P25942: Variant p.Ser39Thr

Tumor necrosis factor receptor superfamily member 5
Gene: CD40
Variant information

Variant position:  39
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 Serine (S) to Threonine (T) at position 39 (S39T, p.Ser39Thr).
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 small size and polar (S) to medium size and polar (T)
The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:  1
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 bladder carcinoma cell line Hu549.
Any additional useful information about the variant.



Sequence information

Variant position:  39
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  277
The length of the canonical sequence.

Location on the sequence:   HPEPPTACREKQYLINSQCC  S LCQPGQKLVSDCTEFTETEC
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                         HPEPPTACREKQYLINSQCCSLCQPGQKLVSDCTEFTETEC

                              YPEPRTACREKQYLVDSQCCNMCPPGEKLVNDCLHTIDTEC

Mouse                         HLGQCVTCSDKQYLHDGQCCDLCQPGSRLTSHCTALEKTQC

Pig                           HPEPPTSCKENQYPTNSRCCNLCPPGQKLVNHCTEVTETEC

Bovine                        HSEPATACGEKQYPVNSLCCDLCPPGQKLVNDCTEVSKTEC

Horse                         HPEQATACKGNQYLSGSHCCDLCPPGKKLVNDCTGITETEC

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 21 – 277 Tumor necrosis factor receptor superfamily member 5
Topological domain 21 – 193 Extracellular
Repeat 25 – 60 TNFR-Cys 1
Disulfide bond 38 – 51


Literature citations

Biochemical characteristics and partial amino acid sequence of the receptor-like human B cell and carcinoma antigen CDw40.
Braesch-Andersen S.; Paulie S.; Koho H.; Nika H.; Aspenstroem P.; Perlmann P.;
J. Immunol. 142:562-567(1989)
Cited for: PROTEIN SEQUENCE OF 21-50; SUBUNIT; VARIANTS GLN-26; GLY-35 AND THR-39;

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.