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UniProtKB/Swiss-Prot Q96JQ0: Variant p.Asn2370Ile

Protocadherin-16
Gene: DCHS1
Chromosomal location: 11p15.4
Variant information

Variant position:  2370
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 Asparagine (N) to Isoleucine (I) at position 2370 (N2370I, p.Asn2370Ile).
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 medium size and polar (N) to medium size and hydrophobic (I)
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

Involvement in disease:  Van Maldergem syndrome 1 (VMLDS1) [MIM:601390]: An autosomal recessive disorder characterized by intellectual disability, typical craniofacial features, auditory malformations resulting in hearing loss, and skeletal and limb malformations. Some patients have renal hypoplasia. Brain MRI typically shows periventricular nodular heterotopia. {ECO:0000269|PubMed:24056717}. 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 VMLDS1.
Any additional useful information about the variant.

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



Sequence information

Variant position:  2370
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  3298
The length of the canonical sequence.

Location on the sequence:   LAHDGPHEGRANLTVLVEDV  N DNAPAFSQSLYQVMLLEHTP
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                         LAHDGPHEGRANLTVLVEDVNDNAPAFSQSLYQVMLLEHTP

Mouse                         LAHDGPHEGHANLTVLVEDVNDNVPTFSQSLYQVMMLEHTP

Rat                           LAHDGPHEGHANLTVLVEDVNDNVPIFSQSLYQVMMLEHTP

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 43 – 3298 Protocadherin-16
Topological domain 43 – 2940 Extracellular
Domain 2278 – 2376 Cadherin 22
Glycosylation 2361 – 2361 N-linked (GlcNAc...) asparagine


Literature citations

Mutations in genes encoding the cadherin receptor-ligand pair DCHS1 and FAT4 disrupt cerebral cortical development.
Cappello S.; Gray M.J.; Badouel C.; Lange S.; Einsiedler M.; Srour M.; Chitayat D.; Hamdan F.F.; Jenkins Z.A.; Morgan T.; Preitner N.; Uster T.; Thomas J.; Shannon P.; Morrison V.; Di Donato N.; Van Maldergem L.; Neuhann T.; Newbury-Ecob R.; Swinkells M.; Terhal P.; Wilson L.C.; Zwijnenburg P.J.; Sutherland-Smith A.J.; Black M.A.; Markie D.; Michaud J.L.; Simpson M.A.; Mansour S.; McNeill H.; Goetz M.; Robertson S.P.;
Nat. Genet. 45:1300-1308(2013)
Cited for: VARIANT VMLDS1 ILE-2370;

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.