UniProtKB/SwissProt variant VAR

Variant information

Variant position:

102

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 Arginine (R) to Glycine (G) at position 102 (R102G, p.Arg102Gly).

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 large size and basic (R) to glycine (G)

The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:

-2

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:

There are two alleles: C3S (C3 slow), the most common allele in all races and C3F (C3 fast), relatively frequent in Caucasians, less common in Black Americans, extremely rare in Orientals.

Additional information on the polymorphism described.

Variant description:

In allele C3F; associated with susceptibility to ARMD9; results in decreased binding affinity for regulator factor H; results in reduced sensitivity to cleavage by factor I.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs2230199 [ dbSNP | Ensembl ]

Sequence information

Variant position:

102

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

Protein sequence length:

1663

The length of the canonical sequence.

Location on the sequence:

HMGNVTFTIPANREFKSEKG R NKFVTVQATFGTQVVEKVVL

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                         HMGNVTFTIPANREFKSEKGRNKFVTVQATFGTQVVEKVVL

Mouse                         HLRSVSIKIPASKEFNSDKEGHKYVTVVANFGETVVEKAVM

Rat                           HLNRVFIKIPASKEFNADK-GHKYVTVVANFGATVVEKAVL

Pig                           YLSTVNIKIPASKEFKSEK-GHKFVTVQALFGNVQVEKVVL

Bovine                        YLSTVTIKIPASKELKSDK-GHKFVTVVATFGNVQVEKVVL

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	23 – 1663	Complement C3
Chain	23 – 667	Complement C3 beta chain
Glycosylation	85 – 85	N-linked (GlcNAc...) asparagine

Literature citations

Submission
SeattleSNPs variation discovery resource;
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]; VARIANTS GLY-102; LEU-314; LYS-863; ASP-1224 AND THR-1367;

Molecular basis of polymorphisms of human complement component C3.
Botto M.; Yong Fong K.; So A.K.; Koch C.; Walport M.J.;
J. Exp. Med. 172:1011-1017(1990)
Cited for: VARIANTS GLY-102 AND LEU-314;

Complement C3 variant and the risk of age-related macular degeneration.
Yates J.R.W.; Sepp T.; Matharu B.K.; Khan J.C.; Thurlby D.A.; Shahid H.; Clayton D.G.; Hayward C.; Morgan J.; Wright A.F.; Armbrecht A.M.; Dhillon B.; Deary I.J.; Redmond E.; Bird A.C.; Moore A.T.;
N. Engl. J. Med. 357:553-561(2007)
Cited for: ASSOCIATION OF VARIANT GLY-102 WITH ARMD9;

Common polymorphisms in C3, factor B, and factor H collaborate to determine systemic complement activity and disease risk.
Heurich M.; Martinez-Barricarte R.; Francis N.J.; Roberts D.L.; Rodriguez de Cordoba S.; Morgan B.P.; Harris C.L.;
Proc. Natl. Acad. Sci. U.S.A. 108:8761-8766(2011)
Cited for: CHARACTERIZATION OF VARIANT GLY-102;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P01024: Variant p.Arg102Gly