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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q9NP85: Variant p.Val180Met

Podocin
Gene: NPHS2
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Variant information Variant position: help 180 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 Valine (V) to Methionine (M) at position 180 (V180M, p.Val180Met). 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 Similar physico-chemical property. Both residues are medium size and hydrophobic. 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 NPHS2. Any additional useful information about the variant.
Other resources: help Links to websites of interest for the variant.


Sequence information Variant position: help 180 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 383 The length of the canonical sequence.
Location on the sequence: help DTYHKVDLRLQTLEIPFHEI V TKDMFIMEIDAICYYRMENA 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                         DTYHKVDLRLQTLEIPFHEIVTKDMFIMEIDAICYYRMENA

Mouse                         DTYHKVDLRLQTLEIPFHEVVTKDMFIMEIDAVCYYRMENA

Rat                           DTYHKVDLRLQTLEIPFHEVVTKDMFIMEIDAVCYYRMENA
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 1 – 383 Podocin
Topological domain 124 – 383 Cytoplasmic
Alternative sequence 179 – 246 Missing. In isoform 2.



Literature citations
NPHS2, encoding the glomerular protein podocin, is mutated in autosomal recessive steroid-resistant nephrotic syndrome.
Boute N.; Gribouval O.; Roselli S.; Benessy F.; Lee H.; Fuchshuber A.; Dahan K.; Gubler M.-C.; Niaudet P.; Antignac C.;
Nat. Genet. 24:349-354(2000)
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA] (ISOFORM 1); VARIANTS NPHS2 RP CYS-92; GLN-138; GLY-160; MET-180 AND TRP-291; VARIANT LEU-20; NPHS2 gene in steroid-resistant nephrotic syndrome: prevalence, clinical course, and mutational spectrum in South-West Iranian children.
Basiratnia M.; Yavarian M.; Torabinezhad S.; Erjaee A.;
Iran. J. Kidney Dis. 7:357-362(2013)
Cited for: VARIANTS NPHS2 LEU-118; GLY-160; CYS-168; MET-180 AND SER-238; A molecular genetic analysis of childhood nephrotic syndrome in a cohort of Saudi Arabian families.
Al-Hamed M.H.; Al-Sabban E.; Al-Mojalli H.; Al-Harbi N.; Faqeih E.; Al Shaya H.; Alhasan K.; Al-Hissi S.; Rajab M.; Edwards N.; Al-Abbad A.; Al-Hassoun I.; Sayer J.A.; Meyer B.F.;
J. Hum. Genet. 58:480-489(2013)
Cited for: VARIANTS NPHS2 39-GLN--LEU-383 DEL; PRO-138; HIS-168; MET-180; PHE-254 AND GLU-260; VARIANT GLN-237;
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.