UniProtKB/Swiss-Prot P12081: Variant p.Ala5Glu

Histidine--tRNA ligase, cytoplasmic
Gene: HARS1
Feedback?

Variant information Variant position:

5 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Type of variant:

LB/B 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 Alanine (A) to Glutamate (E) at position 5 (A5E, p.Ala5Glu). 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 hydrophobic (A) to medium size and acidic (E) The physico-chemical property of the reference and variant residues and the change implicated.
BLOSUM score:

-1 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
Other resources:

Links to websites of interest for the variant.

Variant rs78741041 [ dbSNP | Ensembl ]

Sequence information Variant position:

5 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length:

509 The length of the canonical sequence.
Location on the sequence:

MAER A ALEELVKLQGERVRGLKQQK 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                         MAERAALEELVKLQGERVRGLKQQK

Mouse                         MADRAALEELVRLQGAHVRGLKEQK

Bovine                        MADRAALEDLVRVQGERVRGLKQQK

Zebrafish                     MADKAQLQEAIKTQGEVVRKLKSEK

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
Initiator methionine	1 – 1	Removed
Chain	2 – 509	Histidine--tRNA ligase, cytoplasmic
Domain	3 – 59	WHEP-TRS
Modified residue	2 – 2	N-acetylalanine
Helix	3 – 23

Literature citations
A loss-of-function variant in the human histidyl-tRNA synthetase (HARS) gene is neurotoxic in vivo.
Vester A.; Velez-Ruiz G.; McLaughlin H.M.; Lupski J.R.; Talbot K.; Vance J.M.; Zuchner S.; Roda R.H.; Fischbeck K.H.; Biesecker L.G.; Nicholson G.; Beg A.A.; Antonellis A.;
Hum. Mutat. 34:191-199(2013)
Cited for: INVOLVEMENT IN CMT2W; VARIANTS GLU-5; ASP-205 AND ARG-376; VARIANTS CMT2W GLN-137; ALA-238 AND SER-505; CHARACTERIZATION OF VARIANT CMT2W GLN-137;

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.