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UniProtKB/Swiss-Prot Q7Z494: Variant p.Arg973Gln

Nephrocystin-3
Gene: NPHP3
Variant information

Variant position:  973
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Type of variant:  Disease [Disclaimer]
The variants are classified into three categories: Disease, Polymorphism and Unclassified.
  • Disease: Variants implicated in disease according to literature reports.
  • Polymorphism: Variants not reported to be implicated in disease.
  • Unclassified: Variants with uncertain implication in disease according to literature reports. Evidence against or in favor of a pathogenic role is limited and/or conflicting.

Residue change:  From Arginine (R) to Glutamine (Q) at position 973 (R973Q, p.Arg973Gln).
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 (Q)
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

Involvement in disease:  Renal-hepatic-pancreatic dysplasia 1 (RHPD1) [MIM:208540]: A disease characterized by cystic malformations of the kidneys, liver, and pancreas. The pathological findings consist of multicystic dysplastic kidneys, dilated and dysgenetic bile ducts, a dysplastic pancreas with dilated ducts, cysts, fibrosis and inflammatory infiltrates. {ECO:0000269|PubMed:18371931}. Note=The disease is caused by mutations affecting the gene represented in this entry.
The name and a short description of the disease associated with the variant. For more information about the disease, the user can refer to OMIM, following the link provided after the disease acronym.

Variant description:  In RHPD1.
Any additional useful information about the variant.

Other resources:  
Links to websites of interest for the variant.



Sequence information

Variant position:  973
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  1330
The length of the canonical sequence.

Location on the sequence:   LKDLGLLSQAIVPLQRSLEI  R ETALDPDHPRVAQSLHQLAS
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                         LKDLGLLSQAIVPLQRSLEIRETALDPDHPRVAQSLHQLAS

Mouse                         LKDLGLLSQAVVPLQRSLEIRETALDPDHPRVAQSLHQLAG

Xenopus laevis                LKDLGLLSQAVTPLQRSLEIRETALDPDHPSVAQSLHQLAG

Xenopus tropicalis            LKDLGLLSQAVTPLQRSLEIRETALDPDHPSVAQSLHQLAG

Zebrafish                     LKDLGLLSQAVAPLQRSLEIRETALDPDHPSVAQSLHQLAG

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 2 – 1330 Nephrocystin-3
Repeat 943 – 976 TPR 4
Alternative sequence 151 – 1330 Missing. In isoform 7.
Alternative sequence 182 – 1330 Missing. In isoform 4.
Alternative sequence 240 – 1330 Missing. In isoform 5.
Alternative sequence 637 – 1330 Missing. In isoform 3.
Alternative sequence 705 – 1330 Missing. In isoform 6.


Literature citations

Loss of nephrocystin-3 function can cause embryonic lethality, Meckel-Gruber-like syndrome, situs inversus, and renal-hepatic-pancreatic dysplasia.
Bergmann C.; Fliegauf M.; Bruechle N.O.; Frank V.; Olbrich H.; Kirschner J.; Schermer B.; Schmedding I.; Kispert A.; Kraenzlin B.; Nuernberg G.; Becker C.; Grimm T.; Girschick G.; Lynch S.A.; Kelehan P.; Senderek J.; Neuhaus T.J.; Stallmach T.; Zentgraf H.; Nuernberg P.; Gretz N.; Lo C.; Lienkamp S.; Schaefer T.; Walz G.; Benzing T.; Zerres K.; Omran H.;
Am. J. Hum. Genet. 82:959-970(2008)
Cited for: VARIANT RHPD1 GLN-973; INVOLVEMENT IN MKS7; FUNCTION; INTERACTION WITH INVS;

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.