UniProtKB/SwissProt variant VAR

Variant information

Variant position:

42

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 Phenylalanine (F) to Isoleucine (I) at position 42 (F42I, p.Phe42Ile).

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 large size and aromatic (F) to medium size and hydrophobic (I)

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 COD3; likely benign variant.

Any additional useful information about the variant.

Sequence information

Variant position:

42

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

Protein sequence length:

201

The length of the canonical sequence.

Location on the sequence:

YKKFMTECPSGQLTLYEFRQ F FGLKNLSPSASQYVEQMFET

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                         YKKFMTECPSGQLTLYEFRQFFGLKNLSPSASQYVEQMFET

Mouse                         YKKFMTECPSGQLTLYEFRQFFGLKNLSPSASQYVEQMFET

Bovine                        YKKFMTECPSGQLTLYEFRQFFGLKNLSPWASQYVEQMFET

Chicken                       YKKFMTECPSGQLTLYEFKQFFGLKNLSPSANKYVEQMFET

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	2 – 201	Guanylyl cyclase-activating protein 1
Domain	31 – 49	EF-hand 1

Literature citations

Characterization of GUCA1A-associated dominant cone/cone-rod dystrophy: low prevalence among Japanese patients with inherited retinal dystrophies.
Mizobuchi K.; Hayashi T.; Katagiri S.; Yoshitake K.; Fujinami K.; Yang L.; Kuniyoshi K.; Shinoda K.; Machida S.; Kondo M.; Ueno S.; Terasaki H.; Matsuura T.; Tsunoda K.; Iwata T.; Nakano T.;
Sci. Rep. 9:16851-16851(2019)
Cited for: VARIANTS COD3 ILE-42; GLU-68; ILE-80; ASN-99; SER-99; PHE-151 AND ARG-184;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P43080: Variant p.Phe42Ile