UniProtKB/Swiss-Prot Q9BZW4: Variant p.Glu167Lys

Transmembrane 6 superfamily member 2
Gene: TM6SF2
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Variant information Variant position:

167 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 Glutamate (E) to Lysine (K) at position 167 (E167K, p.Glu167Lys). 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 acidic (E) 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
Variant description:

Associated with higher circulating levels of alanine transaminase with lower levels of low-density lipoprotein-cholesterol (LDL-C), triglycerides and alkaline phosphatase in 3 independent populations; reduces protein expression by 46%. Any additional useful information about the variant.
Other resources:

Links to websites of interest for the variant.

Variant rs58542926 [ dbSNP | Ensembl ]

Sequence information Variant position:

167 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length:

377 The length of the canonical sequence.
Location on the sequence:

SFAMSILVFLTGNILGKYSS E IRPAFFLTIPYLLVPCWAGM 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                         SFAMSILVFLTGNILGKYSSEIRPAFFLTIPYLLVPCWAGM

Mouse                         SFAMSILVFLPGNILGKYSSEMRPTFFLAILYMLVPCWAGV

Rat                           SFAMSLLVFLPGNILGKYSSEIRPTFFLAILYMLVPCWAGM

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 – 377	Transmembrane 6 superfamily member 2
Domain	61 – 186	EXPERA 1

Literature citations
Systematic evaluation of coding variation identifies a candidate causal variant in TM6SF2 influencing total cholesterol and myocardial infarction risk.
Holmen O.L.; Zhang H.; Fan Y.; Hovelson D.H.; Schmidt E.M.; Zhou W.; Guo Y.; Zhang J.; Langhammer A.; Lochen M.L.; Ganesh S.K.; Vatten L.; Skorpen F.; Dalen H.; Zhang J.; Pennathur S.; Chen J.; Platou C.; Mathiesen E.B.; Wilsgaard T.; Njolstad I.; Boehnke M.; Chen Y.E.; Abecasis G.R.; Hveem K.; Willer C.J.;
Nat. Genet. 46:345-351(2014)
Cited for: VARIANT LYS-167; Exome-wide association study identifies a TM6SF2 variant that confers susceptibility to nonalcoholic fatty liver disease.
Kozlitina J.; Smagris E.; Stender S.; Nordestgaard B.G.; Zhou H.H.; Tybjaerg-Hansen A.; Vogt T.F.; Hobbs H.H.; Cohen J.C.;
Nat. Genet. 46:352-356(2014)
Cited for: VARIANT LYS-167; CHARACTERIZATION OF VARIANT LYS-167; TISSUE SPECIFICITY; FUNCTION; TM6SF2 rs58542926 influences hepatic fibrosis progression in patients with non-alcoholic fatty liver disease.
Liu Y.L.; Reeves H.L.; Burt A.D.; Tiniakos D.; McPherson S.; Leathart J.B.; Allison M.E.; Alexander G.J.; Piguet A.C.; Anty R.; Donaldson P.; Aithal G.P.; Francque S.; Van Gaal L.; Clement K.; Ratziu V.; Dufour J.F.; Day C.P.; Daly A.K.; Anstee Q.M.;
Nat. Commun. 5:4309-4309(2014)
Cited for: VARIANT LYS-167;

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.