UniProtKB/SwissProt variant VAR

Variant information

Variant position:

1970

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

Type of variant:

LP/P [Disclaimer]

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 Leucine (L) to Phenylalanine (F) at position 1970 (L1970F, p.Leu1970Phe).

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 (L) to large size and aromatic (F)

The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:

0

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 ARMD2 and FFM.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs28938473 [ dbSNP | Ensembl ]

Sequence information

Variant position:

1970

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:

TSSPAVDRLCVGVRPGECFG L LGVNGAGKTTTFKMLTGDTT

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                         TSSPAVDRLCVGVRPGECFGLLGVNGAGKTTTFKMLTGDTT

Mouse                         SSSPAVDRLCVGVRPGECFGLLGVNGAGKTTTFKMLTGDTT

Slime mold                    KSKIAVYNSTLAIPTGQTFGLLGLNGCGKSTTLGMISGEIS

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	1895 – 2273	Cytoplasmic
Domain	1938 – 2170	ABC transporter 2
Mutagenesis	1975 – 1975	G -> D. Inhibition of retinal-stimulated ATP hydrolysis.
Mutagenesis	1978 – 1978	K -> M. Inhibition of retinal-stimulated ATP hydrolysis.
Mutagenesis	1978 – 1978	K -> M. Inhibits ATPase activity; when associated with M-969. Decreases translocase activity; when associated with M-969. Does not affect protein subcellular localization in endoplasmic reticulum; when associated with M-969.

Literature citations

Spectrum of ABCR gene mutations in autosomal recessive macular dystrophies.
Rozet J.-M.; Gerber S.; Souied E.; Perrault I.; Chatelin S.; Ghazi I.; Leowski C.; Dufier J.-L.; Munnich A.; Kaplan J.;
Eur. J. Hum. Genet. 6:291-295(1998)
Cited for: VARIANTS STGD1 TRP-18; CYS-212; HIS-636; MET-1019; VAL-1038; CYS-1108; TRP-1640; SER-1977 AND HIS-2107; VARIANTS FFM PRO-11; PRO-541; VAL-1038; GLU-1091; CYS-1508; PHE-1970 AND ARG-1971;

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;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P78363: Variant p.Leu1970Phe