UniProtKB/Swiss-Prot Q9BQ52: Variant p.Ala541Thr

Zinc phosphodiesterase ELAC protein 2
Gene: ELAC2
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Variant information Variant position:

541 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 Alanine (A) to Threonine (T) at position 541 (A541T, p.Ala541Thr). 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 polar (T) 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 HPC2; risk factor for disease development; does not affect the enzymatic activity. Any additional useful information about the variant.
Other resources:

Links to websites of interest for the variant.

Variant rs5030739 [ dbSNP | Ensembl ]

Sequence information Variant position:

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

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

FGQLCRHYGDQVDRVLGTLA A VFVSHLHADHHTGLPSILLQ 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                         FGQLCRHYGDQ-VDRVLGTLAAVFVSHLHADHHTGLPSILLQ

Gorilla                       FGQLCRHYGDQ-VDRVLGTLAAVFVSHLHADHHTGLLNILL

Chimpanzee                    FGQLCRHYGDQ-VDRVLGTLAAVFVSHLHADHHTGLLNILL

Mouse                         FGQLCRHYGQQ-IDRVLCSLTAVFVSHLHADHHTGLLNILL

Rat                           FGQLCRHYGQQ-IDRVLCNLTAVFVSHLHADHHTGLLNILL

Caenorhabditis elegans        YGQMRAVFGEDGCKQLLVNLNCVLITHAHQDHMNGLYTIIA

Fission yeast                 ISQFFRQYGTN-TEPMLRKLKAIFITHLHSDHYLGLLNVLQ

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	17 – 826	Zinc phosphodiesterase ELAC protein 2

Literature citations
A candidate prostate cancer susceptibility gene at chromosome 17p.
Tavtigian S.V.; Simard J.; Teng D.H.F.; Abtin V.; Baumgard M.; Beck A.; Camp N.J.; Carillo A.R.; Chen Y.; Dayananth P.; Desrochers M.; Dumont M.; Farnham J.M.; Frank D.; Frye C.; Ghaffari S.; Gupte J.S.; Hu R.; Iliev D.; Janecki T.; Kort E.N.; Laity K.E.; Leavitt A.; Leblanc G.; McArthur-Morrison J.; Pederson A.; Penn B.; Peterson K.T.; Reid J.E.; Richards S.; Schroeder M.; Smith R.; Snyder S.C.; Swedlund B.; Swensen J.; Thomas A.; Tranchant M.; Woodland A.-M.; Labrie F.; Skolnick M.H.; Neuhausen S.; Rommens J.; Cannon-Albright L.A.;
Nat. Genet. 27:172-180(2001)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1); TISSUE SPECIFICITY; VARIANTS HPC2 LEU-217; THR-541 AND HIS-781; A candidate prostate cancer susceptibility gene encodes tRNA 3' processing endoribonuclease.
Takaku H.; Minagawa A.; Takagi M.; Nashimoto M.;
Nucleic Acids Res. 31:2272-2278(2003)
Cited for: ENZYME ACTIVITY; CHARACTERIZATION OF VARIANTS HPC2 LEU-217; THR-541 AND HIS-781; Association of HPC2/ELAC2 genotypes and prostate cancer.
Rebbeck T.R.; Walker A.H.; Zeigler-Johnson C.; Weisburg S.; Martin A.-M.; Nathanson K.L.; Wein A.J.; Malkowicz S.B.;
Am. J. Hum. Genet. 67:1014-1019(2000)
Cited for: VARIANTS HPC2 LEU-217 AND THR-541; Role of HPC2/ELAC2 in hereditary prostate cancer.
Wang L.; McDonnell S.K.; Elkins D.A.; Slager S.L.; Christensen E.; Marks A.F.; Cunningham J.M.; Peterson B.J.; Jacobsen S.J.; Cerhan J.R.; Blute M.L.; Schaid D.J.; Thibodeau S.N.;
Cancer Res. 61:6494-6499(2001)
Cited for: VARIANTS HPC2 GLN-211; LEU-217; ARG-487; THR-541 AND ARG-806; Association of common missense changes in ELAC2 (HPC2) with prostate cancer in a Japanese case-control series.
Fujiwara H.; Emi M.; Nagai H.; Nishimura T.; Konishi N.; Kubota Y.; Ichikawa T.; Takahashi S.; Shuin T.; Habuchi T.; Ogawa O.; Inoue K.; Skolnick M.H.; Swensen J.; Camp N.J.; Tavtigian S.V.;
J. Hum. Genet. 47:641-648(2002)
Cited for: VARIANTS HPC2 LEU-217 AND THR-541; Meta-analysis of associations of the Ser217Leu and Ala541Thr variants in ELAC2 (HPC2) and prostate cancer.
Camp N.J.; Tavtigian S.V.;
Am. J. Hum. Genet. 71:1475-1478(2002)
Cited for: VARIANTS HPC2 LEU-217 AND THR-541; ELAC2/HPC2 polymorphisms, prostate-specific antigen levels, and prostate cancer.
Severi G.; Giles G.G.; Southey M.C.; Tesoriero A.; Tilley W.; Neufing P.; Morris H.; English D.R.; McCredie M.R.; Boyle P.; Hopper J.L.;
J. Natl. Cancer Inst. 95:818-824(2003)
Cited for: VARIANTS HPC2 LEU-217 AND THR-541;

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.