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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot O60500: Variant p.Pro519Ser

Nephrin
Gene: NPHS1
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Variant information Variant position: help 519 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 Proline (P) to Serine (S) at position 519 (P519S, p.Pro519Ser). 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 hydrophobic (P) to small size and polar (S) The physico-chemical property of the reference and variant residues and the change implicated.
BLOSUM score: help -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: help In NPHS1. Any additional useful information about the variant.
Other resources: help Links to websites of interest for the variant.


Sequence information Variant position: help 519 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 1241 The length of the canonical sequence.
Location on the sequence: help LGSVEKSGSTFSRELVLVTG P SDNQAKFTCKAGQLSASTQL 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                         LGSVEKSGSTFSRELVLVTGPSDNQAKFTCKAGQLSASTQL

Mouse                         LGSVEKSGSTFSRELVLIIGPPDNLAKFSCKAGQLSASTQL

Rat                           LGSVEKSGSTFSRELVLIIGPPDNRAKFSCKAGQLSASTQL
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 23 – 1241 Nephrin
Topological domain 23 – 1055 Extracellular
Domain 440 – 540 Ig-like C2-type 5
Disulfide bond 465 – 528



Literature citations
Thirteen novel NPHS1 mutations in a large cohort of children with congenital nephrotic syndrome.
Heeringa S.F.; Vlangos C.N.; Chernin G.; Hinkes B.; Gbadegesin R.; Liu J.; Hoskins B.E.; Ozaltin F.; Hildebrandt F.;
Nephrol. Dial. Transplant. 23:3527-3533(2008)
Cited for: VARIANTS NPHS1 TRP-256; CYS-367; CYS-412; SER-519; ARG-569 AND GLY-709;
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.