UniProtKB/SwissProt variant VAR

Variant information

Variant position:

122

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 Glycine (G) to Aspartate (D) at position 122 (G122D, p.Gly122Asp).

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 glycine (G) to medium size and acidic (D)

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

Other resources:

Links to websites of interest for the variant.

Variant rs61748441 [ dbSNP | Ensembl ]

Sequence information

Variant position:

122

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

Protein sequence length:

299

The length of the canonical sequence.

Location on the sequence:

KQQQQPPGGQAKARPAKRKA G TSPRPSTDVCPDPLGISDSY

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                         KQQQQPPGGQAKARPAKRKAGTSPRPSTDVCPDPLGISDSY

                              KEQPQPPGAQTKARPAKRKAGMSPRSSSDVCPDPLGISDSY

Mouse                         KQQQQPPGAQTKARPAKRKAGTSPRPSTDVCTDPLGISDSY

Bovine                        KQQQQPPGAQAKARPAKRKAGTSPRSSTDVCPDPLGISDSY

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 – 299	Cone-rod homeobox protein
Region	93 – 155	Disordered

Literature citations

Prevalence of mutations causing retinitis pigmentosa and other inherited retinopathies.
Sohocki M.M.; Daiger S.P.; Bowne S.J.; Rodriquez J.A.; Northrup H.; Heckenlively J.R.; Birch D.G.; Mintz-Hittner H.; Ruiz R.S.; Lewis R.A.; Saperstein D.A.; Sullivan L.S.;
Hum. Mutat. 17:42-51(2001)
Cited for: VARIANTS ASP-10; ILE-66; ASP-122 AND THR-158; VARIANTS RP GLN-41 AND GLN-115;

Analysis of protein-coding genetic variation in 60,706 humans.
Lek M.; Karczewski K.J.; Minikel E.V.; Samocha K.E.; Banks E.; Fennell T.; O'Donnell-Luria A.H.; Ware J.S.; Hill A.J.; Cummings B.B.; Tukiainen T.; Birnbaum D.P.; Kosmicki J.A.; Duncan L.E.; Estrada K.; Zhao F.; Zou J.; Pierce-Hoffman E.; Berghout J.; Cooper D.N.; Deflaux N.; DePristo M.; Do R.; Flannick J.; Fromer M.; Gauthier L.; Goldstein J.; Gupta N.; Howrigan D.; Kiezun A.; Kurki M.I.; Moonshine A.L.; Natarajan P.; Orozco L.; Peloso G.M.; Poplin R.; Rivas M.A.; Ruano-Rubio V.; Rose S.A.; Ruderfer D.M.; Shakir K.; Stenson P.D.; Stevens C.; Thomas B.P.; Tiao G.; Tusie-Luna M.T.; Weisburd B.; Won H.H.; Yu D.; Altshuler D.M.; Ardissino D.; Boehnke M.; Danesh J.; Donnelly S.; Elosua R.; Florez J.C.; Gabriel S.B.; Getz G.; Glatt S.J.; Hultman C.M.; Kathiresan S.; Laakso M.; McCarroll S.; McCarthy M.I.; McGovern D.; McPherson R.; Neale B.M.; Palotie A.; Purcell S.M.; Saleheen D.; Scharf J.M.; Sklar P.; Sullivan P.F.; Tuomilehto J.; Tsuang M.T.; Watkins H.C.; Wilson J.G.; Daly M.J.; MacArthur D.G.;
Nature 536:285-291(2016)
Cited for: VARIANT ASP-122;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot O43186: Variant p.Gly122Asp