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UniProtKB/Swiss-Prot Q8IWN7: Variant p.Thr1954Ala

Retinitis pigmentosa 1-like 1 protein
Gene: RP1L1
Variant information

Variant position:  1954
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 Threonine (T) to Alanine (A) at position 1954 (T1954A, p.Thr1954Ala).
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 polar (T) to small size and hydrophobic (A)
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

Polymorphism:  The exact length of RP1L1 is variable between individuals due to the presence of several length polymorphisms. The sequence shown here is that of allele RP1L1-1 and includes 3 repeats (from aa 1292-1342) with a length of 16 amino acids. The number of repeats is highly polymorphic and varies among different alleles, ranging from 3 to 8.
Additional information on the polymorphism described.

Other resources:  
Links to websites of interest for the variant.



Sequence information

Variant position:  1954
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  2400
The length of the canonical sequence.

Location on the sequence:   ESEGAEAQEAEEAAQEAEGQ  T QPESEVIESQEAEEEAQPES
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                         ESEGAEAQEAEEAAQEAEGQTQPESEVIESQEAEEEAQPES

Mouse                         -----------------------------------------

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.

TypePositionsDescription
Chain 1 – 2400 Retinitis pigmentosa 1-like 1 protein
Repeat 1939 – 1954 2-7
Region 1697 – 2400 Disordered
Region 1836 – 2244 25 X 16 AA approximate tandem repeats of [ED]-[AT]-[PQ]-[ED]-[AVT]-E-[GKE]-[ED]-[AMT]-Q-[EPK]-[EAT]-[TSELP]-[EG]-[EGSQDI]-[AVIE]
Coiled coil 1934 – 2017
Alternative sequence 223 – 2400 Missing. In isoform 2.


Literature citations

Characterization of RP1L1, a highly polymorphic paralog of the retinitis pigmentosa 1 (RP1) gene.
Bowne S.J.; Daiger S.P.; Malone K.A.; Heckenlively J.R.; Kennan A.; Humphries P.; Hughbanks-Wheaton D.; Birch D.G.; Liu Q.; Pierce E.A.; Zuo J.; Huang Q.; Donovan D.D.; Sullivan L.S.;
Mol. Vis. 9:129-137(2003)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ALLELES RP1L1-1; RP1L1-2; RP1L1-3; RP1L1-4; RP1L1-5 AND RP1L1-6; ISOFORM 1); VARIANTS PRO-792; TRP-1146; SER-1285; GLY-1319; SER-1467; GLU-1946; ALA-1954; LYS-2171 AND GLY-2242; POLYMORPHISM;

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.