UniProtKB/Swiss-Prot P08100: Variant p.Val104Ile

Rhodopsin
Gene: RHO
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Variant information Variant position:

104 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 Valine (V) to Isoleucine (I) at position 104 (V104I, p.Val104Ile). 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:

Similar physico-chemical property. Both residues are medium size and hydrophobic. The physico-chemical property of the reference and variant residues and the change implicated.
BLOSUM score:

3 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:

Found in patients with pathologic myopia; uncertain significance. Any additional useful information about the variant.
Other resources:

Links to websites of interest for the variant.

Variant rs144317206 [ dbSNP | Ensembl ]

Sequence information Variant position:

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

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

LFMVLGGFTSTLYTSLHGYF V FGPTGCNLEGFFATLGGEIA 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                         LFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIA

                              LFMVFGGFTTTLYTSLHGYFVFGPTGCNVEGFFATLGGEIA

Mouse                         LFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIA

Rat                           LFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIG

Pig                           LFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIA

Bovine                        LFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIA

Rabbit                        LFMVLGGFTTTLYTSLHGYFVFGPTGCNVEGFFATLGGEIA

Sheep                         LFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIA

Cat                           LFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIA

Chicken                       LFMVFGGFTTTMYTSMNGYFVFGVTGCYIEGFFATLGGEIA

Xenopus laevis                HFMVLCGFTVTMYTSMHGYFIFGPTGCYIEGFFATLGGEVA

Zebrafish                     LFMVFGGFTTTMYTSLHGYFVFGRLGCNLEGFFATLGGEMG

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 – 348	Rhodopsin
Topological domain	97 – 110	Extracellular
Site	113 – 113	Plays an important role in the conformation switch to the active conformation
Mutagenesis	113 – 113	E -> Q. Induces a conformation change that promotes interaction with GRK1 and SAG; when associated with Y-257.

Literature citations
Identification of novel rhodopsin mutations responsible for retinitis pigmentosa: implications for the structure and function of rhodopsin.
Macke J.P.; Davenport C.M.; Jacobson S.G.; Hennessey J.C.; Gonzalez-Fernandez F.; Conway B.P.; Heckenlively J.; Palmer R.; Maumenee I.H.; Sieving P.; Gouras P.; Good W.; Nathans J.;
Am. J. Hum. Genet. 53:80-89(1993)
Cited for: VARIANTS RP4 ARG-106; GLY-135; SER-140; GLU-188 AND ARG-211; VARIANTS ALA-51; ILE-104 AND MET-209; A novel potentially causative variant of NDUFAF7 revealed by mutation screening in a chinese family with pathologic myopia.
Wang B.; Liu Y.; Chen S.; Wu Y.; Lin S.; Duan Y.; Zheng K.; Zhang L.; Gu X.; Hong W.; Shao H.; Zeng X.; Sun B.; Duan S.;
Invest. Ophthalmol. Vis. Sci. 58:4182-4192(2017)
Cited for: VARIANT ILE-104;

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.