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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P29400: Variant p.Cys1678Trp

Collagen alpha-5(IV) chain
Gene: COL4A5
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Variant information Variant position: help 1678 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Type of variant: help 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: help From Cysteine (C) to Tryptophan (W) at position 1678 (C1678W, p.Cys1678Trp). 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: help Change from medium size and polar (C) to large size and aromatic (W) The physico-chemical property of the reference and variant residues and the change implicated.
BLOSUM score: help -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
Variant description: help In ATS1. Any additional useful information about the variant.
Other resources: help Links to websites of interest for the variant.


Sequence information Variant position: help 1678 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 1685 The length of the canonical sequence.
Location on the sequence: help FSKPQSETLKAGDLRTRISR C QVCMKRT 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: help The multiple alignment of the region surrounding the variant against various orthologous sequences. 
Human                         FSKPQSETLKAGDLRTRISRCQVCMKRT

                              FSKPQSETLKAGDLRTRISRCQVCMKRT
Sequence annotation in neighborhood: help 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 27 – 1685 Collagen alpha-5(IV) chain
Domain 1461 – 1685 Collagen IV NC1
Disulfide bond 1586 – 1681 Or C-1586 with C-1678
Disulfide bond 1620 – 1678 Or C-1620 with C-1681
Cross 1667 – 1667 S-Lysyl-methionine sulfilimine (Lys-Met) (interchain with M-1549)
Beta strand 1677 – 1683



Literature citations
Detection of mutations in the COL4A5 gene in over 90% of male patients with X-linked Alport's syndrome by RT-PCR and direct sequencing.
Inoue Y.; Nishio H.; Shirakawa T.; Nakanishi K.; Nakamura H.; Sumino K.; Nishiyama K.; Iijima K.; Yoshikawa N.;
Am. J. Kidney Dis. 34:854-862(1999)
Cited for: VARIANTS ATS1 GLU-579; LYS-633; ASP-947; VAL-953; ARG-1107; ARG-1158; SER-1170 AND TRP-1678; VARIANTS SER-444 AND ALA-739;
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.