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UniProtKB/Swiss-Prot O60931: Variant p.Thr260Ile

Cystinosin
Gene: CTNS
Variant information

Variant position:  260
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 Threonine (T) to Isoleucine (I) at position 260 (T260I, p.Thr260Ile).
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 polar (T) to medium size and hydrophobic (I)
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

Variant description:  Slightly decreased cystine transport.
Any additional useful information about the variant.

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



Sequence information

Variant position:  260
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  367
The length of the canonical sequence.

Location on the sequence:   FLVLAWLFAFVTMIVAAVGV  T TWLQFLFCFSYIKLAVTLVK
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                         FLVLAWLFAFVTMIVAAVGVTTWLQFLFCFSYIKLAVTLVK

Mouse                         FLVLAWLFVLVTMIVAAVGITTWLQFLFCFSYIKLIITLIK

Bovine                        FLVLSWLFTLIALIMAAVGATTWLQFLFCFSYIKLAVTLVK

Caenorhabditis elegans        LMIVLISFGFCSAAATVLRKIQLLSFVTSLSYIKMAVTCCK

Drosophila                    ILAIFAVVVVVSAGLAGGSVIHWLDFLYYCSYVKLTITIIK

Slime mold                    IATLIWVSLIVMTILGFSNVFTWLWVINYYSYVKLFITFIK

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 23 – 367 Cystinosin
Topological domain 259 – 261 Lumenal
Mutagenesis 270 – 270 S -> T. Gain-of-function mutant that shows higher transport of cystine.
Mutagenesis 274 – 274 L -> F. Gain-of-function mutant that shows higher transport of cystine.


Literature citations

A novel gene encoding an integral membrane protein is mutated in nephropathic cystinosis.
Town M.; Jean G.; Cherqui S.; Attard M.; Forestier L.; Whitmore S.A.; Callen D.F.; Gribouval O.; Broyer M.; Bates G.P.; van 't Hoff W.; Antignac C.;
Nat. Genet. 18:319-324(1998)
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA] (ISOFORM 1); VARIANT ILE-260;

The genomic region encompassing the nephropathic cystinosis gene (CTNS): complete sequencing of a 200-kb segment and discovery of a novel gene within the common cystinosis-causing deletion.
Touchman J.W.; Anikster Y.; Dietrich N.L.; Maduro V.V.B.; McDowell G.; Shotelersuk V.; Bouffard G.G.; Beckstrom-Sternberg S.M.; Gahl W.A.; Green E.D.;
Genome Res. 10:165-173(2000)
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]; VARIANT ILE-260;

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] (ISOFORM 2); VARIANT ILE-260;

Submission
Mural R.J.; Istrail S.; Sutton G.G.; Florea L.; Halpern A.L.; Mobarry C.M.; Lippert R.; Walenz B.; Shatkay H.; Dew I.; Miller J.R.; Flanigan M.J.; Edwards N.J.; Bolanos R.; Fasulo D.; Halldorsson B.V.; Hannenhalli S.; Turner R.; Yooseph S.; Lu F.; Nusskern D.R.; Shue B.C.; Zheng X.H.; Zhong F.; Delcher A.L.; Huson D.H.; Kravitz S.A.; Mouchard L.; Reinert K.; Remington K.A.; Clark A.G.; Waterman M.S.; Eichler E.E.; Adams M.D.; Hunkapiller M.W.; Myers E.W.; Venter J.C.;
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]; VARIANT ILE-260;

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] (ISOFORM 2); VARIANT ILE-260;

Identification and detection of the common 65-kb deletion breakpoint in the nephropathic cystinosis gene (CTNS).
Anikster Y.; Lucero C.; Touchman J.W.; Huizing M.; McDowell G.; Shotelersuk V.; Green E.D.; Gahl W.A.;
Mol. Genet. Metab. 66:111-116(1999)
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 228-367; VARIANT ILE-260;

Mutational spectrum of the CTNS gene in Italy.
Mason S.; Pepe G.; Dall'Amico R.; Tartaglia S.; Casciani S.; Greco M.; Bencivenga P.; Murer L.; Rizzoni G.; Tenconi R.; Clementi M.;
Eur. J. Hum. Genet. 11:503-508(2003)
Cited for: VARIANTS CTNS ILE-287; ARG-308; ARG-337 AND ARG-339; VARIANT ILE-260;

Molecular pathogenesis of cystinosis: effect of CTNS mutations on the transport activity and subcellular localization of cystinosin.
Kalatzis V.; Nevo N.; Cherqui S.; Gasnier B.; Antignac C.;
Hum. Mol. Genet. 13:1361-1371(2004)
Cited for: FUNCTION; SUBCELLULAR LOCATION; CHARACTERIZATION OF VARIANTS CTNS VAL-110; PHE-133; PHE-139; PHE-141; PRO-158; ASP-169; SER-177; ARG-182; ASN-205; ASP-205 DEL; ARG-222; SER-270 DEL; LYS-288; ASN-298; TYR-305; ARG-308; PRO-338; ARG-339; 343-ILE--ASP-346 DEL; ASP-346--349-PHE DEL AND ASP-VAL-GLU-PHE-349 INS; CHARACTERIZATION OF VARIANT CTNSJAN 67-ILE--PRO-73 DEL; PRO-CYS-SER-154 INS; LEU-200; ARG-280; LYS-323 AND ASN-346; CHARACTERIZATION OF VARIANT CTNSANN ARG-197; CHARACTERIZATION OF VARIANT ILE-42 AND ILE-260;

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.