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UniProtKB/Swiss-Prot Q8NF91: Variant p.Leu3892Ser

Gene: SYNE1
Variant information

Variant position:  3892
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Type of variant:  US
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:  From Leucine (L) to Serine (S) at position 3892 (L3892S, p.Leu3892Ser).
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 hydrophobic (L) to small size and polar (S)
The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:  -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:  Found in a patient with mild intellectual disability, spastic paraplegia, axon neuropathy and leukoencephalopathy; unknown pathological significance.
Any additional useful information about the variant.

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

Sequence information

Variant position:  3892
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  8797
The length of the canonical sequence.

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.



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.

Chain 1 – 8797 Nesprin-1
Topological domain 1 – 8746 Cytoplasmic
Repeat 3815 – 3920 Spectrin 34
Coiled coil 314 – 8666
Alternative sequence 1 – 7843 Missing. In isoform 9.
Alternative sequence 1 – 7838 Missing. In isoform 3.
Alternative sequence 1 – 7658 Missing. In isoform 11.
Alternative sequence 1 – 5585 Missing. In isoform 8.
Alternative sequence 1 – 5476 Missing. In isoform 2.
Alternative sequence 1444 – 8797 Missing. In isoform 5.
Alternative sequence 1726 – 8797 Missing. In isoform 6.
Alternative sequence 3050 – 8797 Missing. In isoform 10.
Alternative sequence 3395 – 8797 Missing. In isoform GSRP-56.

Literature citations

Identification of pathogenic gene variants in small families with intellectually disabled siblings by exome sequencing.
Schuurs-Hoeijmakers J.H.; Vulto-van Silfhout A.T.; Vissers L.E.; van de Vondervoort I.I.; van Bon B.W.; de Ligt J.; Gilissen C.; Hehir-Kwa J.Y.; Neveling K.; del Rosario M.; Hira G.; Reitano S.; Vitello A.; Failla P.; Greco D.; Fichera M.; Galesi O.; Kleefstra T.; Greally M.T.; Ockeloen C.W.; Willemsen M.H.; Bongers E.M.; Janssen I.M.; Pfundt R.; Veltman J.A.; Romano C.; Willemsen M.A.; van Bokhoven H.; Brunner H.G.; de Vries B.B.; de Brouwer A.P.;
J. Med. Genet. 50:802-811(2013)
Cited for: VARIANTS ARG-655; THR-3088 AND SER-3892;

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.