UniProtKB/Swiss-Prot P78363: Variant p.Ile1562Thr

Retinal-specific phospholipid-transporting ATPase ABCA4
Gene: ABCA4
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Variant information Variant position:

1562 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Type of variant:

US 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 1562 (I1562T, p.Ile1562Thr). 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
Variant description:

In STGD1, FFM, ARMD2 and CORD3; uncertain significance. Any additional useful information about the variant.
Other resources:

Links to websites of interest for the variant.

Variant rs1762111 [ dbSNP | Ensembl ]

Sequence information Variant position:

1562 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length:

2273 The length of the canonical sequence.
Location on the sequence:

IRSSLKSKFWVNEQRYGGIS I GGKLPVVPITGEALVGFLSD 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                         IRSSLKSKFWVNEQRYGGISIGGKLPVVPITGEALVGFLSD

Mouse                         IRSSLKSKFWVNEQRYGGISIGGKLPAIPISGEALVGFLSG

Bovine                        IRSSLKSKFWVNEQRYGGISVGGKLPAPPFTGEALVGFLSD

Slime mold                    ------------------FGVPGAL-------------YFD

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	1 – 2273	Retinal-specific phospholipid-transporting ATPase ABCA4
Topological domain	1398 – 1727	Extracellular
Beta strand	1558 – 1562

Literature citations
Mutation of the Stargardt disease gene (ABCR) in age-related macular degeneration.
Allikmets R.; Shroyer N.F.; Singh N.; Seddon J.M.; Lewis R.A.; Bernstein P.S.; Peiffer A.; Zabriskie N.A.; Li Y.; Hutchinson A.; Dean M.; Lupski J.R.; Leppert M.;
Science 277:1805-1807(1997)
Cited for: REVIEW; VARIANTS ARMD2 LYS-471; LEU-1129; SER-1517; THR-1562; ARG-1578; HIS-1898; PHE-1970 AND ASN-2177; VARIANTS GLY-643; HIS-846; ALA-863; GLN-943; MET-1428; GLU-1961 AND ILE-2255; A comprehensive survey of sequence variation in the ABCA4 (ABCR) gene in Stargardt disease and age-related macular degeneration.
Rivera A.; White K.; Stoehr H.; Steiner K.; Hemmrich N.; Grimm T.; Jurklies B.; Lorenz B.; Scholl H.P.N.; Apfelstedt-Sylla E.; Weber B.H.F.;
Am. J. Hum. Genet. 67:800-813(2000)
Cited for: VARIANTS STGD1 GLU-60; THR-60; GLU-65; LEU-68; ARG-72; CYS-212; SER-230; SER-247; VAL-328; LYS-471; PRO-541; GLN-572; ARG-607; LYS-635; CYS-653; TYR-764; ARG-765; ALA-901; ILE-959; LYS-1036; VAL-1038; PRO-1063; ASP-1087; CYS-1097; CYS-1108; LEU-1380; LYS-1399; PRO-1430; VAL-1440; HIS-1443; LEU-1486; TYR-1488; MET-1537; PRO-1689; LEU-1705; THR-1733; ARG-1748; PRO-1763; LYS-1885; HIS-1898; GLU-1961; ARG-1975; SER-1977; GLY-2077; TRP-2077 AND VAL-2241; VARIANTS GLN-152; HIS-212; ARG-423; ILE-552; ARG-914; GLN-943; THR-1562; ILE-1868; MET-1921; LEU-1948; PHE-1970; ALA-2059; ASN-2177 AND VAL-2216; Late-onset Stargardt disease is associated with missense mutations that map outside known functional regions of ABCR (ABCA4).
Yatsenko A.N.; Shroyer N.F.; Lewis R.A.; Lupski J.R.;
Hum. Genet. 108:346-355(2001)
Cited for: VARIANTS FFM GLY-339; ALA-863; TRP-943; ARG-991; VAL-1038; CYS-1108; ARG-1488; THR-1562; GLN-1640; PHE-2027; GLN-2030 AND CYS-2106; VARIANTS HIS-212; ARG-423; GLN-943; THR-1148; ILE-1868 AND ILE-2255; Mutations in ABCR (ABCA4) in patients with Stargardt macular degeneration or cone-rod degeneration.
Briggs C.E.; Rucinski D.; Rosenfeld P.J.; Hirose T.; Berson E.L.; Dryja T.P.;
Invest. Ophthalmol. Vis. Sci. 42:2229-2236(2001)
Cited for: VARIANTS STGD1 13-LYS--TRP-15 DEL; TYR-54; LYS-58; VAL-60; GLU-65; GLU-77; HIS-190; PRO-244; ARG-309; CYS-525; CYS-537; PRO-541; PRO-549; ARG-550; GLN-602; ARG-607; MET-643; ASP-767; PRO-797; ARG-821; THR-824; ALA-863; ALA-935; TRP-943; ALA-989; VAL-1038; CYS-1108; LEU-1108; LYS-1122; ARG-1201; GLN-1300; LEU-1380; PRO-1388; ARG-1408; LEU-1486; ARG-1488; TYR-1490; MET-1526; ASN-1532; THR-1562; TRP-1640; LEU-1776; THR-1846; GLU-1961; SER-1977; PHE-2027; GLN-2030; PRO-2035; LEU-2050; CYS-2107; HIS-2107; TRP-2139; ARG-2150 AND TYR-2150; VARIANTS CORD3 GLN-1640 AND ASP-2146; VARIANTS HIS-212; ARG-423; GLN-943; THR-1637; ILE-1868 AND LEU-1948; Detection rate of pathogenic mutations in ABCA4 using direct sequencing: clinical and research implications.
Downes S.M.; Packham E.; Cranston T.; Clouston P.; Seller A.; Nemeth A.H.;
Arch. Ophthalmol. 130:1486-1490(2012)
Cited for: VARIANTS 219-ARG--ASP-2273 DEL; HIS-576; GLN-943; ARG-1488; MET-1526; CYS-1557; THR-1562; GLU-1773; ASP-1794; 2040-ARG--ASP-2273 DEL AND CYS-2107; VARIANTS STGD1 TYR-54; GLN-152; ARG-184; PHE-184; CYS-212; SER-418; LYS-471; MET-643; CYS-653; 782-TRP--ASP-2273 DEL; ALA-863; ALA-989; ARG-991; MET-1019; LYS-1022; SER-1097; CYS-1108; LYS-1122; LEU-1129; ARG-1201; LEU-1380; LYS-1442; LEU-1486; TYR-1490; ASP-1598; ASP-1754; THR-1846; GLU-1961; PHE-2027; GLN-2030; CYS-2106; LYS-2131; TYR-2150 AND PRO-2237;

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