UniProtKB/SwissProt variant VAR

Variant information

Variant position:

339

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 339 (R339C, p.Arg339Cys).

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 PLS.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs1044703733 [ dbSNP | Ensembl ]

Sequence information

Variant position:

339

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

Protein sequence length:

463

The length of the canonical sequence.

Location on the sequence:

EACFPYTGTDSPCKMKEDCF R YYSSEYHYVGGFYGGCNEAL

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                         EACFPYTGTDSPCKMKEDCFRYYSSEYHYVGGFYGGCNEAL

Mouse                         ESCFPYTAKDSPCKPRENCLRYYSSDYYYVGGFYGGCNEAL

Rat                           ENCFPYTATDAPCKPKENCLRYYSSEYYYVGGFYGGCNEAL

Bovine                        EDCFPYTGTDSPCRLKEGCFRYYSSEYHYVGGFYGGCNEAL

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	231 – 394	Dipeptidyl peptidase 1 heavy chain
Binding site	347 – 347	Chloride
Alternative sequence	138 – 463	Missing. In isoform 2.
Alternative sequence	142 – 463	Missing. In isoform 3.

Literature citations

Loss-of-function mutations in the cathepsin C gene result in periodontal disease and palmoplantar keratosis.
Toomes C.; James J.; Wood A.J.; Wu C.L.; McCormick D.; Lench N.; Hewitt C.; Moynihan L.; Roberts E.; Woods C.G.; Markham A.; Wong M.; Widmer R.; Ghaffar K.A.; Pemberton M.; Hussein I.R.; Temtamy S.A.; Davies R.; Read A.P.; Sloan P.; Dixon M.J.; Thakker N.S.;
Nat. Genet. 23:421-424(1999)
Cited for: VARIANTS PLS PHE-249; LEU-252; PRO-272; SER-301; CYS-339 AND CYS-347;

Localisation of a gene for prepubertal periodontitis to chromosome 11q14 and identification of a cathepsin C gene mutation.
Hart T.C.; Hart P.S.; Michalec M.D.; Zhang Y.; Marazita M.L.; Cooper M.; Yassin O.M.; Nusier M.; Walker S.;
J. Med. Genet. 37:95-101(2000)
Cited for: VARIANTS PLS CYS-339 AND CYS-340; VARIANT AP1 CYS-347;

Identification of cathepsin C mutations in ethnically diverse Papillon-Lefevre syndrome patients.
Hart P.S.; Zhang Y.; Firatli E.; Uygur C.; Lotfazar M.; Michalec M.D.; Marks J.J.; Lu X.; Coates B.J.; Seow W.K.; Marshall R.; Williams D.; Reed J.B.; Wright J.T.; Hart T.C.;
J. Med. Genet. 37:927-932(2000)
Cited for: VARIANTS PLS 67-TYR--ALA-74 DEL; PRO-272; SER-300; VAL-301; SER-301; ASN-304; GLY-319; CYS-339; CYS-340 AND GLY-447; VARIANT THR-153;

Novel point mutations, deletions, and polymorphisms in the cathepsin C gene in nine families from Europe and North Africa with Papillon-Lefevre syndrome.
Lefevre C.; Blanchet-Bardon C.; Jobard F.; Bouadjar B.; Stalder J.-F.; Cure S.; Hoffmann A.; Prud'Homme J.-F.; Fischer J.;
J. Invest. Dermatol. 117:1657-1661(2001)
Cited for: VARIANTS PLS PRO-127; PRO-272; CYS-339 AND CYS-429; VARIANTS THR-153 AND LYS-401;

The role of cathepsin C in Papillon-Lefevre syndrome, prepubertal periodontitis, and aggressive periodontitis.
Hewitt C.; McCormick D.; Linden G.; Turk D.; Stern I.; Wallace I.; Southern L.; Zhang L.; Howard R.; Bullon P.; Wong M.; Widmer R.; Gaffar K.A.; Awawdeh L.; Briggs J.; Yaghmai R.; Jabs E.W.; Hoeger P.; Bleck O.; Rudiger S.G.; Petersilka G.; Battino M.; Brett P.; Hattab F.; Al-Hamed M.; Sloan P.; Toomes C.; Dixon M.J.; James J.; Read A.P.; Thakker N.S.;
Hum. Mutat. 23:222-228(2004)
Cited for: VARIANTS PLS GLU-129; ARG-139; TYR-236; PHE-249; LEU-252; HIS-272; SER-301; ARG-312; CYS-339; CYS-347 AND GLY-447; VARIANTS AP1 HIS-272 AND CYS-412; VARIANT THR-153;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P53634: Variant p.Arg339Cys