UniProtKB/SwissProt variant VAR

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.

Variant rs180727534 [ dbSNP | Ensembl ]

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.

Location on the sequence:

SVKSVREKGEALLELVQDVT L KDKIDQLQSDYQDLCSIGKE

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                         SVKSVREKGEALLELVQDVTLKDKIDQLQSDYQDLCSIGKE

Mouse                         SVTSVQEKSEALLELVQDQSLKDKIQKLQSDFQDLCSRAKE

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.

Type	Positions	Description
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;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q8NF91: Variant p.Leu3892Ser