UniProtKB/SwissProt variant VAR

Variant information

Variant position:

125

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

Type of variant:

Disease [Disclaimer]

The variants are classified into three categories: Disease, Polymorphism and Unclassified.

Disease: Variants implicated in disease according to literature reports.
Polymorphism: Variants not reported to be implicated in disease.
Unclassified: Variants with uncertain implication in disease according to literature reports. Evidence against or in favor of a pathogenic role is limited and/or conflicting.

Residue change:

From Valine (V) to Methionine (M) at position 125 (V125M, p.Val125Met).

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:

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

Involvement in disease:

Senior-Loken syndrome 9 (SLSN9) [MIM:616629]: A renal-retinal disorder characterized by progressive wasting of the filtering unit of the kidney (nephronophthisis), with or without medullary cystic renal disease, and progressive eye disease. Typically this disorder becomes apparent during the first year of life. {ECO:0000269|PubMed:26487268}. Note=The disease is caused by mutations affecting the gene represented in this entry.

The name and a short description of the disease associated with the variant. For more information about the disease, the user can refer to OMIM, following the link provided after the disease acronym.

Variant description:

In SLSN9; results in altered folding of the N-terminus; does not localize to the ciliary tip and transition zone; does not affect interaction with IFT20; loss of interaction with MAP4.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs886037898 [ dbSNP | Ensembl ]

Sequence information

Variant position:

125

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

Protein sequence length:

691

The length of the canonical sequence.

Location on the sequence:

NELLQIIGKCCLNKLSSDDA V RRVLAGEKGEVKGRASLTSR

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                         NELLQIIGKCCLNKLSSDDAVRRVLAGEKGEVKGRASLTSR

Mouse                         NELLQLIGKCCLSKLSSDEAVKRVLAGDKGDSRGRAQRTSK

Rat                           NELLQLIGKCCLSKLSSDEAVKRVLAGEKGDSRGRVLRTSK

Zebrafish                     NELLQVIAKCCLNKLSSDEAVKRVLAGDKLDQKGKPS-TSR

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 – 691	TRAF3-interacting protein 1
Region	1 – 323	Abolishes microtubules-binding when missing
Helix	123 – 130

Literature citations

Mutations in TRAF3IP1/IFT54 reveal a new role for IFT proteins in microtubule stabilization.
Bizet A.A.; Becker-Heck A.; Ryan R.; Weber K.; Filhol E.; Krug P.; Halbritter J.; Delous M.; Lasbennes M.C.; Linghu B.; Oakeley E.J.; Zarhrate M.; Nitschke P.; Garfa-Traore M.; Serluca F.; Yang F.; Bouwmeester T.; Pinson L.; Cassuto E.; Dubot P.; Elshakhs N.A.; Sahel J.A.; Salomon R.; Drummond I.A.; Gubler M.C.; Antignac C.; Chibout S.; Szustakowski J.D.; Hildebrandt F.; Lorentzen E.; Sailer A.W.; Benmerah A.; Saint-Mezard P.; Saunier S.;
Nat. Commun. 6:8666-8666(2015)
Cited for: FUNCTION; SUBCELLULAR LOCATION; INVOLVEMENT IN SLSN9; VARIANTS SLSN9 SER-17; ALA-125; MET-125 AND ARG-520; CHARACTERIZATION OF VARIANTS SLSN9 SER-17; ALA-125; MET-125 AND ARG-520;

UniProtKB/Swiss-Prot Q8TDR0: Variant p.Val125Met