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UniProtKB/Swiss-Prot P54803: Variant p.Ile562Thr

Galactocerebrosidase
Gene: GALC
Chromosomal location: 14q31
Variant information

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

Type of variant:  Polymorphism
The variants are classified into three categories: Disease, Polymorphism and Unclassified.
  • Disease: Variants implicated in disease according to literature reports.
  • Polymorphism: Variants not reported to be implicated in disease.
  • Unclassified: Variants with uncertain implication in disease according to literature reports. Evidence against or in favor of a pathogenic role is limited and/or conflicting.

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.

Variant description:  Common polymorphism.
Any additional useful information about the variant.

Other resources:  
Links to websites of interest for the variant.



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                         AADASNTISIIGDYNWTNLTIKCDVYIETPDTG-GVFIAGRV

                              AADAYNTISIIGDYKWSNLTVRCDVYIETPEKG-GVFIAGR

Rhesus macaque                AADASNTISIIGDYNWTNLTIKCDVYIETPDTG-GVFIAGR

Mouse                         AADASSTISVIGDHHWTNMTVQCDVYIETPRSG-GVFIAGR

Xenopus laevis                ASDANQAISVIGNYQWSNITVTCDIYIETVETG-GVFVAAR

Xenopus tropicalis            ASDANQAISVIGNYQWSNVTVTSDIYIETPDTG-GVFVAAR

Zebrafish                     AKDADQTISIIGDYSWSDVNVSCDVFIETPKTG-GVFLAAR

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.

TypePositionsDescription
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 GLD 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 GLD 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 GLD 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;

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.