UniProtKB/SwissProt variant VAR

Variant information

Variant position:

44

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 Aspartate (D) to Valine (V) at position 44 (D44V, p.Asp44Val).

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 acidic (D) to medium size and hydrophobic (V)

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

Variant description:

In SMA3; impairs GEMIN2 binding.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs104893931 [ dbSNP | Ensembl ]

Sequence information

Variant position:

44

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

Protein sequence length:

294

The length of the canonical sequence.

Location on the sequence:

GTGQSDDSDIWDDTALIKAY D KAVASFKHALKNGDICETSG

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                         GTGQSDDSDIWDDTALIKAYDKAVASFKHAL--KNGDICETSG

                              GTGQSDDSDIWDDTALIKAYDKAVASFKHAL--KNGDISEA

Mouse                         GTGQSDDSDIWDDTALIKAYDKAVASFKHAL--KNGDICET

Rat                           GTGQSDDSDIWDDTALIKAYDKAVASFKHAL--KNGDMCET

Bovine                        GTGESDDSDVWDDTALIKAYDKAVASFKHAL--KNGDISEA

Cat                           GTGQSDDSDIWDDTALIKAYDKAVASFKHAL--KNGDISEA

Drosophila                    -MSDETNAAVWDDSLLVKTYDESVGLAREALARRLADSTNK

Fission yeast                 --MDQSQKEVWDDSELRNAFETALHEFKKYH----------

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	2 – 294	Survival motor neuron protein
Region	26 – 51	Interacts with GEMIN2
Modified residue	25 – 25	Phosphothreonine
Modified residue	28 – 28	Phosphoserine
Modified residue	31 – 31	Phosphoserine
Cross	51 – 51	Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)
Mutagenesis	34 – 34	W -> A. Impairs GEMIN2 binding.
Mutagenesis	39 – 39	L -> A. Impairs GEMIN2 binding.
Mutagenesis	43 – 43	Y -> A. Impairs GEMIN2 binding.
Mutagenesis	44 – 44	D -> A. Impairs GEMIN2 binding.
Mutagenesis	46 – 46	A -> N. Impairs GEMIN2 binding.
Helix	38 – 48

Literature citations

Structure of a key intermediate of the SMN complex reveals Gemin2's crucial function in snRNP assembly.
Zhang R.; So B.R.; Li P.; Yong J.; Glisovic T.; Wan L.; Dreyfuss G.;
Cell 146:384-395(2011)
Cited for: X-RAY CRYSTALLOGRAPHY (2.50 ANGSTROMS) OF 26-62 IN COMPLEX WITH SNRPD1; SNRPD2; SNRPE; SNRPF; SNRPG AND GEMIN2; FUNCTION; SUBUNIT; INTERACTION WITH GEMIN2; VARIANT SMA3 VAL-44; MUTAGENESIS OF ASP-44;

Molecular and functional analysis of intragenic SMN1 mutations in patients with spinal muscular atrophy.
Sun Y.; Grimmler M.; Schwarzer V.; Schoenen F.; Fischer U.; Wirth B.;
Hum. Mutat. 25:64-71(2005)
Cited for: VARIANTS SMA1/SMA2/SMA3 ASN-30; VAL-44; ARG-95; GLY-111; GLY-262; CYS-272 AND ILE-274; CHARACTERIZATION OF VARIANTS SMA1/SMA2/SMA3 ASN-30; VAL-44; ARG-95 AND GLY-111;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q16637: Variant p.Asp44Val