UniProtKB/Swiss-Prot A1A4Y4: Variant p.Thr94Lys

• Variant information
• Sequence information
• Literature citations
• All

Variant information

Variant position: 94 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 Lysine (K) at position 94 (T94K, p.Thr94Lys). 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 large size and basic (K) 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
Polymorphism: Genetic variations in the IRGM promoter determine Mycobacterium tuberculosis susceptibility [MIM:607948] (PubMed:19750224). People that are homozygote for -261C-T (rs9637876) variant, which is located within an Alu sequence in the promoter region, are associated with protection from M.tuberculosis (PubMed:19750224). In contrast, -261T-T allele is significantly associated with protection from pulmonary tuberculosis caused by M.tuberculosis, but not by M.africanum, a strain restricted to West Africa, or M.bovis (PubMed:19750224). Additional information on the polymorphism described.
Other resources: Links to websites of interest for the variant.

• Variant rs72553867 [ dbSNP | Ensembl ]

Sequence information

Variant position: 94 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: 181 The length of the canonical sequence.
Location on the sequence: RCASYFSSHFSNVVLWDLPG T GSATTTLENYLMEMQFNRYD 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.
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 – 181	Immunity-related GTPase family M protein
Domain	32 – 181	IRG-type G

Literature citations

Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility.
Parkes M.; Barrett J.C.; Prescott N.J.; Tremelling M.; Anderson C.A.; Fisher S.A.; Roberts R.G.; Nimmo E.R.; Cummings F.R.; Soars D.; Drummond H.; Lees C.W.; Khawaja S.A.; Bagnall R.; Burke D.A.; Todhunter C.E.; Ahmad T.; Onnie C.M.; McArdle W.; Strachan D.; Bethel G.; Bryan C.; Lewis C.M.; Deloukas P.; Forbes A.; Sanderson J.; Jewell D.P.; Satsangi J.; Mansfield J.C.; Cardon L.; Mathew C.G.;
Nat. Genet. 39:830-832(2007)
Cited for: INVOLVEMENT IN IBD19; VARIANTS ASP-17 AND LYS-94; TISSUE SPECIFICITY;