UniProtKB/Swiss-Prot P54803: Variant p.Ile562Thr

Galactocerebrosidase
Gene: GALC
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Variant information Variant position:

562 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 Isoleucine (I) to Threonine (T) at position 562 (I562T, p.Ile562Thr). 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 (I) to medium size and polar (T) 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
Polymorphism:

Polymorphic amino-acid changes are responsible for the wide range of catalytic activities found in the general population. Additional information on the polymorphism described.
Other resources:

Links to websites of interest for the variant.

Variant rs398607 [ dbSNP | Ensembl ]

Sequence information Variant position:

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

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

AADASNTISIIGDYNWTNLT I KCDVYIETPDTGGVFIAGRV 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                         AADASNTISIIGDYNWTNLTIKCDVYIETPDTGGVFIAG-RV

                              AADAYNTISIIGDYKWSNLTVRCDVYIETPEKGGVFIAG-R

Rhesus macaque                AADASNTISIIGDYNWTNLTIKCDVYIETPDTGGVFIAG-R

Mouse                         AADASSTISVIGDHHWTNMTVQCDVYIETPRSGGVFIAG-R

Xenopus laevis                ASDANQAISVIGNYQWSNITVTCDIYIETVETGGVFVAA-R

Xenopus tropicalis            ASDANQAISVIGNYQWSNVTVTSDIYIETPDTGGVFVAA-R

Zebrafish                     AKDADQTISIIGDYSWSDVNVSCDVFIETPKTGGVFLAA-R

Caenorhabditis elegans        CTSHIRTPYAVMAYRKKNSILNAEVNIPKHSTAKSIILGIR

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	43 – 685	Galactocerebrosidase
Glycosylation	556 – 556	N-linked (GlcNAc...) asparagine
Glycosylation	559 – 559	N-linked (GlcNAc...) asparagine

Literature citations
Structure and organization of the human galactocerebrosidase (GALC) gene.
Luzi P.; Rafi M.A.; Wenger D.A.;
Genomics 26:407-409(1995)
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]; VARIANT THR-562; Complete sequencing and characterization of 21,243 full-length human cDNAs.
Ota T.; Suzuki Y.; Nishikawa T.; Otsuki T.; Sugiyama T.; Irie R.; Wakamatsu A.; Hayashi K.; Sato H.; Nagai K.; Kimura K.; Makita H.; Sekine M.; Obayashi M.; Nishi T.; Shibahara T.; Tanaka T.; Ishii S.; Yamamoto J.; Saito K.; Kawai Y.; Isono Y.; Nakamura Y.; Nagahari K.; Murakami K.; Yasuda T.; Iwayanagi T.; Wagatsuma M.; Shiratori A.; Sudo H.; Hosoiri T.; Kaku Y.; Kodaira H.; Kondo H.; Sugawara M.; Takahashi M.; Kanda K.; Yokoi T.; Furuya T.; Kikkawa E.; Omura Y.; Abe K.; Kamihara K.; Katsuta N.; Sato K.; Tanikawa M.; Yamazaki M.; Ninomiya K.; Ishibashi T.; Yamashita H.; Murakawa K.; Fujimori K.; Tanai H.; Kimata M.; Watanabe M.; Hiraoka S.; Chiba Y.; Ishida S.; Ono Y.; Takiguchi S.; Watanabe S.; Yosida M.; Hotuta T.; Kusano J.; Kanehori K.; Takahashi-Fujii A.; Hara H.; Tanase T.-O.; Nomura Y.; Togiya S.; Komai F.; Hara R.; Takeuchi K.; Arita M.; Imose N.; Musashino K.; Yuuki H.; Oshima A.; Sasaki N.; Aotsuka S.; Yoshikawa Y.; Matsunawa H.; Ichihara T.; Shiohata N.; Sano S.; Moriya S.; Momiyama H.; Satoh N.; Takami S.; Terashima Y.; Suzuki O.; Nakagawa S.; Senoh A.; Mizoguchi H.; Goto Y.; Shimizu F.; Wakebe H.; Hishigaki H.; Watanabe T.; Sugiyama A.; Takemoto M.; Kawakami B.; Yamazaki M.; Watanabe K.; Kumagai A.; Itakura S.; Fukuzumi Y.; Fujimori Y.; Komiyama M.; Tashiro H.; Tanigami A.; Fujiwara T.; Ono T.; Yamada K.; Fujii Y.; Ozaki K.; Hirao M.; Ohmori Y.; Kawabata A.; Hikiji T.; Kobatake N.; Inagaki H.; Ikema Y.; Okamoto S.; Okitani R.; Kawakami T.; Noguchi S.; Itoh T.; Shigeta K.; Senba T.; Matsumura K.; Nakajima Y.; Mizuno T.; Morinaga M.; Sasaki M.; Togashi T.; Oyama M.; Hata H.; Watanabe M.; Komatsu T.; Mizushima-Sugano J.; Satoh T.; Shirai Y.; Takahashi Y.; Nakagawa K.; Okumura K.; Nagase T.; Nomura N.; Kikuchi H.; Masuho Y.; Yamashita R.; Nakai K.; Yada T.; Nakamura Y.; Ohara O.; Isogai T.; Sugano S.;
Nat. Genet. 36:40-45(2004)
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 4 AND 5); NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 2-685 (ISOFORM 3); VARIANTS CYS-184 AND THR-562; The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).
The MGC Project Team;
Genome Res. 14:2121-2127(2004)
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 15-685 (ISOFORM 1); VARIANT THR-562; Molecular heterogeneity of late-onset forms of globoid-cell leukodystrophy.
De Gasperi R.; Gama Sosa M.A.; Sartorato E.L.; Battistini S.; MacFarlane H.; Gusella J.F.; Krivit W.; Kolodny E.H.;
Am. J. Hum. Genet. 59:1233-1242(1996)
Cited for: VARIANTS KRB HIS-79; SER-111; LEU-117; THR-250; SER-284 AND CYS-314; VARIANT THR-562; Adult onset globoid cell leukodystrophy (Krabbe disease): analysis of galactosylceramidase cDNA from four Japanese patients.
Furuya H.; Kukita Y.-J.; Nagano S.; Sakai Y.; Yamashita Y.; Fukuyama H.; Inatomi Y.; Saito Y.; Koike R.; Tsuji S.; Fukumaki Y.; Hayashi K.; Kobayashi T.;
Hum. Genet. 100:450-456(1997)
Cited for: VARIANTS KRB MET-82; ASP-286 AND SER-634; VARIANTS VAL-305 AND THR-562; Identification and characterization of 15 novel GALC gene mutations causing Krabbe disease.
Tappino B.; Biancheri R.; Mort M.; Regis S.; Corsolini F.; Rossi A.; Stroppiano M.; Lualdi S.; Fiumara A.; Bembi B.; Di Rocco M.; Cooper D.N.; Filocamo M.;
Hum. Mutat. 31:E1894-E1914(2010)
Cited for: VARIANTS KRB LYS-130; ARG-318; ARG-323; THR-384; LEU-396 AND ASN-490; VARIANTS PRO-21; CYS-184; ASN-248; THR-562 AND ALA-641;

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