UniProtKB/SwissProt variant VAR

Variant information

Variant position:

2

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

Type of variant:

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:

From Serine (S) to Glycine (G) at position 2 (S2G, p.Ser2Gly).

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 small size and polar (S) to glycine (G)

The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:

0

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:

In NSLH1; creates a N-myristoylation site, resulting in myristoylation of the protein and aberrant targeting to the plasma membrane.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs267607048 [ dbSNP | Ensembl ]

Sequence information

Variant position:

2

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

Protein sequence length:

582

The length of the canonical sequence.

Location on the sequence:

M S SSLGKEKDSKEKDPKVPSAK

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                         MSSSLGKEKDSKEKDPKVPS-AK

Mouse                         MSSSLGKEKDSKEKDPKVPS-A

Rat                           MSSSLGKEKDSKEKDPKVPS-A

Bovine                        MSSSLGKEKDSKEKDPKAPS-A

Chicken                       MSSNLGKEKDCKEKDPKVPS-S

Xenopus laevis                -----MSSSAGKDKEPKVSSGT

Zebrafish                     MSSTLGKDKDSKEREPKA----

Caenorhabditis elegans        -------METSKEFEFRP---A

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 – 582	Leucine-rich repeat protein SHOC-2
Region	1 – 88	Disordered
Compositional bias	1 – 56	Basic and acidic residues

Literature citations

Mutation of SHOC2 promotes aberrant protein N-myristoylation and causes Noonan-like syndrome with loose anagen hair.
Cordeddu V.; Di Schiavi E.; Pennacchio L.A.; Ma'ayan A.; Sarkozy A.; Fodale V.; Cecchetti S.; Cardinale A.; Martin J.; Schackwitz W.; Lipzen A.; Zampino G.; Mazzanti L.; Digilio M.C.; Martinelli S.; Flex E.; Lepri F.; Bartholdi D.; Kutsche K.; Ferrero G.B.; Anichini C.; Selicorni A.; Rossi C.; Tenconi R.; Zenker M.; Merlo D.; Dallapiccola B.; Iyengar R.; Bazzicalupo P.; Gelb B.D.; Tartaglia M.;
Nat. Genet. 41:1022-1026(2009)
Cited for: INVOLVEMENT IN NSLH1; VARIANT NSLH1 GLY-2; CHARACTERIZATION OF VARIANT NSLH1 GLY-2; SUBCELLULAR LOCATION;

Expanding the SHOC2 mutation associated phenotype of Noonan syndrome with loose anagen hair: structural brain anomalies and myelofibrosis.
Gripp K.W.; Zand D.J.; Demmer L.; Anderson C.E.; Dobyns W.B.; Zackai E.H.; Denenberg E.; Jenny K.; Stabley D.L.; Sol-Church K.;
Am. J. Med. Genet. A 161A:2420-2430(2013)
Cited for: VARIANT NSLH1 GLY-2;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q9UQ13: Variant p.Ser2Gly