UniProtKB/Swiss-Prot P16070: Variant p.Ile479Thr

CD44 antigen
Gene: CD44
Feedback?

Variant information Variant position:

479 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 479 (I479T, p.Ile479Thr). 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:

CD44 is responsible for the Indian blood group system. The molecular basis of the In(A)=In1/In(B)=In2 blood group antigens is a single variation in position 46; In(B), the most frequent allele, has Arg-46. Additional information on the polymorphism described.
Other resources:

Links to websites of interest for the variant.

Variant rs1467558 [ dbSNP | Ensembl ]

Sequence information Variant position:

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

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

HPMGRGHQAGRRMDMDSSHS I TLQPTANPNTGLVEDLDRTG 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                         HPMGRGHQAGRRMDMDSSHSITLQPTANPNTGLVEDLDRTG

Mouse                         HPMGQGHQTESK-DTDSSHSTTLQPTAAPNTHLVEDLNRTG

Rat                           HPMGQG-----------------------------------

Bovine                        ---GRSY----------------------------------

Horse                         ---GRAQ----------------------------------

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	21 – 742	CD44 antigen
Topological domain	21 – 649	Extracellular
Region	224 – 649	Stem
Region	372 – 558	Disordered
Compositional bias	473 – 491	Polar residues
Alternative sequence	30 – 742	Missing. In isoform 2.
Alternative sequence	140 – 742	Missing. In isoform 19.
Alternative sequence	223 – 535	Missing. In isoform 11.
Alternative sequence	224 – 604	Missing. In isoform 12, isoform 15 and isoform 18.

Literature citations
The hematopoietic and epithelial forms of CD44 are distinct polypeptides with different adhesion potentials for hyaluronate-bearing cells.
Stamenkovic I.; Aruffo A.; Amiot M.; Seed B.;
EMBO J. 10:343-348(1991)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 10); VARIANT THR-479; Molecular cloning of CD44R1 and CD44R2, two novel isoforms of the human CD44 lymphocyte 'homing' receptor expressed by hemopoietic cells.
Dougherty G.J.; Lansdorp P.M.; Cooper D.L.; Humphries R.K.;
J. Exp. Med. 174:1-5(1991)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 10 AND 11); VARIANT THR-479; The core protein of epican, a heparan sulfate proteoglycan on keratinocytes, is an alternative form of CD44.
Kugelman L.C.; Ganguly S.; Haggerty J.G.; Weissman S.M.; Milstone L.M.;
J. Invest. Dermatol. 99:886-891(1992)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 4); VARIANT THR-479; Genomic structure of DNA encoding the lymphocyte homing receptor CD44 reveals at least 12 alternatively spliced exons.
Screaton G.R.; Bell M.V.; Jackson D.G.; Cornelis F.B.; Gerth U.; Bell J.I.;
Proc. Natl. Acad. Sci. U.S.A. 89:12160-12164(1992)
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]; ALTERNATIVE SPLICING; VARIANTS ARG-417 AND THR-479; CD44: a multitude of isoforms with diverse functions.
Gunthert U.;
Curr. Top. Microbiol. Immunol. 184:47-63(1993)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1); VARIANTS ARG-417; THR-479 AND HIS-494; Novel variants of CD44 arising from alternative splicing: changes in the CD44 alternative splicing pattern of MCF-7 breast carcinoma cells treated with hyaluronidase.
Tanabe K.K.; Nishi T.; Saya H.;
Mol. Carcinog. 7:212-220(1993)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 2; 13 AND 14); VARIANT THR-479; Sequence analysis of the human CD44 antigen.
Wiebe G.J.; Freund D.; Corbeil D.;
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 10 AND 12); VARIANT THR-479; 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] (ISOFORMS 4 AND 12); VARIANTS ARG-417 AND THR-479; Human keratinocytes express a new CD44 core protein (CD44E) as a heparan-sulfate intrinsic membrane proteoglycan with additional exons.
Brown T.A.; Bouchard T.; St John T.; Wayner E.; Carter W.G.;
J. Cell Biol. 113:207-221(1991)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 184-625 (ISOFORM 10); VARIANT THR-479;

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.