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UniProtKB/Swiss-Prot Q9NPF4: Variant p.Ile14Phe

Probable tRNA N6-adenosine threonylcarbamoyltransferase
Gene: OSGEP
Variant information

Variant position:  14
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Type of variant:  LP/P [Disclaimer]
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 Isoleucine (I) to Phenylalanine (F) at position 14 (I14F, p.Ile14Phe).
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 hydrophobic (I) to large size and aromatic (F)
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 GAMOS3; strongly reduced formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs.
Any additional useful information about the variant.

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



Sequence information

Variant position:  14
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  335
The length of the canonical sequence.

Location on the sequence:   MPAVLGFEGSANK  I GVGVVRDGKVLANPRRTYVT
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                         MPAVLGFEGSANKIGVGVVRD-GKVLANPRRTYVT

Mouse                         MPAVLGFEGSANKIGVGVVRD-GTVLANPRRTYV

Rat                           MPAVLGFEGSANKIGVGVVRD-GTVLANPRRTYV

Bovine                        MPAVLGFEGSANKIGVGVVRD-GKVLANPRRTYV

Xenopus laevis                MTIVVGFEGSANKIGVGIIQD-GKVLSNPRRTYI

Zebrafish                     MTIVIGFEGSANKIGIGIIKD-GEVLSNPRRTYI

Drosophila                    MVCALGIEGSANKIGIGIIRD-GKVLANVRRTYI

Slime mold                    MVYIMGFEGSANKLGIGIVKDDGTILSNIRHTFI

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 – 335 Probable tRNA N6-adenosine threonylcarbamoyltransferase
Beta strand 10 – 20


Literature citations

Mutations in KEOPS-complex genes cause nephrotic syndrome with primary microcephaly.
Braun D.A.; Rao J.; Mollet G.; Schapiro D.; Daugeron M.C.; Tan W.; Gribouval O.; Boyer O.; Revy P.; Jobst-Schwan T.; Schmidt J.M.; Lawson J.A.; Schanze D.; Ashraf S.; Ullmann J.F.P.; Hoogstraten C.A.; Boddaert N.; Collinet B.; Martin G.; Liger D.; Lovric S.; Furlano M.; Guerrera I.C.; Sanchez-Ferras O.; Hu J.F.; Boschat A.C.; Sanquer S.; Menten B.; Vergult S.; De Rocker N.; Airik M.; Hermle T.; Shril S.; Widmeier E.; Gee H.Y.; Choi W.I.; Sadowski C.E.; Pabst W.L.; Warejko J.K.; Daga A.; Basta T.; Matejas V.; Scharmann K.; Kienast S.D.; Behnam B.; Beeson B.; Begtrup A.; Bruce M.; Ch'ng G.S.; Lin S.P.; Chang J.H.; Chen C.H.; Cho M.T.; Gaffney P.M.; Gipson P.E.; Hsu C.H.; Kari J.A.; Ke Y.Y.; Kiraly-Borri C.; Lai W.M.; Lemyre E.; Littlejohn R.O.; Masri A.; Moghtaderi M.; Nakamura K.; Ozaltin F.; Praet M.; Prasad C.; Prytula A.; Roeder E.R.; Rump P.; Schnur R.E.; Shiihara T.; Sinha M.D.; Soliman N.A.; Soulami K.; Sweetser D.A.; Tsai W.H.; Tsai J.D.; Topaloglu R.; Vester U.; Viskochil D.H.; Vatanavicharn N.; Waxler J.L.; Wierenga K.J.; Wolf M.T.F.; Wong S.N.; Leidel S.A.; Truglio G.; Dedon P.C.; Poduri A.; Mane S.; Lifton R.P.; Bouchard M.; Kannu P.; Chitayat D.; Magen D.; Callewaert B.; van Tilbeurgh H.; Zenker M.; Antignac C.; Hildebrandt F.;
Nat. Genet. 49:1529-1538(2017)
Cited for: FUNCTION; SUBCELLULAR LOCATION; IDENTIFICATION IN THE EKC/KEOPS COMPLEX; INVOLVEMENT IN GAMOS3; VARIANTS GAMOS3 PHE-14; GLU-78; MET-107; ARG-110; THR-111; THR-139; ALA-177; ARG-198; GLN-247; CYS-280; HIS-280; LEU-280; GLN-325 AND TRP-325; CHARACTERIZATION OF VARIANTS GAMOS3 PHE-14; ARG-110; THR-111; ARG-198; GLN-247; LEU-280 AND GLN-325;

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.