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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q9Y3C8: Variant p.Thr106Ile

Ubiquitin-fold modifier-conjugating enzyme 1
Gene: UFC1
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Variant information Variant position: help 106 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Type of variant: help 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: help From Threonine (T) to Isoleucine (I) at position 106 (T106I, p.Thr106Ile). 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: help Change from medium size and polar (T) to medium size and hydrophobic (I) The physico-chemical property of the reference and variant residues and the change implicated.
BLOSUM score: help -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
Variant description: help In NEDSG; decreased ability to form thioester bond with UFM1; decreased protein ufmylation. Any additional useful information about the variant.
Other resources: help Links to websites of interest for the variant.


Sequence information Variant position: help 106 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 167 The length of the canonical sequence.
Location on the sequence: help IPITYPTTAPEIAVPELDGK T AKMYRGGKICLTDHFKPLWA 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: help The multiple alignment of the region surrounding the variant against various orthologous sequences. 
Human                         IPITYPTTAPEIAVPELDGKTAKMYRGGKICLTDHFKPLWA

Mouse                         IPITYPTTAPEIAVPELDGKTAKMYRGGKICLTDHFKPLWA

Rat                           IPITYPTTAPEIAVPELDGKTAKMYRGGKICLTDHFKPLWA

Bovine                        IPITYPTTAPEIAVPELDGKTAKMYRGGKICLTDHFKPLWA

Zebrafish                     IPVTYPATAPEVAIPELDGKTAKMYRGGKICLTDHFKPLWA

Caenorhabditis elegans        IPITYPVTAPEIALPELDGKTAKMYRGGKICLSEHFKPLWA

Drosophila                    IPVTYPTTAPEIALPELDGKTAKMYRGGKICLTDHFKPLWA

Slime mold                    MPVTYPETAPEIAIPELDGKTEKMYRGGKICLTIHFKPLWS
Sequence annotation in neighborhood: help 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 – 167 Ubiquitin-fold modifier-conjugating enzyme 1
Active site 116 – 116 Glycyl thioester intermediate
Cross 122 – 122 Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in UFM1)
Mutagenesis 108 – 108 K -> A. Abolished ufmylation.
Mutagenesis 110 – 110 Y -> A. Decreased UFM1 transfer.
Mutagenesis 116 – 116 C -> S. Instead of the formation of an intermediate complex with a thiol ester bond between UFC1 (E2-like enzyme) and UFM1 (substrate), a stable complex with an O-ester bond is formed.
Mutagenesis 121 – 121 F -> A. Decreased UFM1 transfer.



Literature citations
Biallelic UFM1 and UFC1 mutations expand the essential role of ufmylation in brain development.
Nahorski M.S.; Maddirevula S.; Ishimura R.; Alsahli S.; Brady A.F.; Begemann A.; Mizushima T.; Guzman-Vega F.J.; Obata M.; Ichimura Y.; Alsaif H.S.; Anazi S.; Ibrahim N.; Abdulwahab F.; Hashem M.; Monies D.; Abouelhoda M.; Meyer B.F.; Alfadhel M.; Eyaid W.; Zweier M.; Steindl K.; Rauch A.; Arold S.T.; Woods C.G.; Komatsu M.; Alkuraya F.S.;
Brain 141:1934-1945(2018)
Cited for: FUNCTION; INTERACTION WITH UFM1; INTERACTION WITH UBA5; MUTAGENESIS OF CYS-116; ACTIVE SITE; INVOLVEMENT IN NEDSG; VARIANTS NEDSG GLN-23 AND ILE-106; CHARACTERIZATION OF VARIANTS NEDSG GLN-23 AND ILE-106; A non-canonical scaffold-type E3 ligase complex mediates protein UFMylation.
Peter J.J.; Magnussen H.M.; DaRosa P.A.; Millrine D.; Matthews S.P.; Lamoliatte F.; Sundaramoorthy R.; Kopito R.R.; Kulathu Y.;
EMBO J. 41:e111015-e111015(2022)
Cited for: FUNCTION; MUTAGENESIS OF LYS-108; CHARACTERIZATION OF VARIANT NEDSG ILE-106;
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.