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UniProtKB/Swiss-Prot P0C7Q2: Variant p.Ala69Ser

Age-related maculopathy susceptibility protein 2
Gene: ARMS2
Variant information

Variant position:  69
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 Alanine (A) to Serine (S) at position 69 (A69S, p.Ala69Ser).
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 small size and hydrophobic (A) to small size and polar (S)
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

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



Sequence information

Variant position:  69
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  107
The length of the canonical sequence.

Location on the sequence:   EGASDKQRSKLSLSHSMIPA  A KIHTELCLPAFFSPAGTQRR
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.

TypePositionsDescription
Chain 1 – 107 Age-related maculopathy susceptibility protein 2


Literature citations

Hypothetical LOC387715 is a second major susceptibility gene for age-related macular degeneration, contributing independently of complement factor H to disease risk.
Rivera A.; Fisher S.A.; Fritsche L.G.; Keilhauer C.N.; Lichtner P.; Meitinger T.; Weber B.H.F.;
Hum. Mol. Genet. 14:3227-3236(2005)
Cited for: SUBCELLULAR LOCATION; INVOLVEMENT IN ARMD8; VARIANT SER-69;

A variant of mitochondrial protein LOC387715/ARMS2, not HTRA1, is strongly associated with age-related macular degeneration.
Kanda A.; Chen W.; Othman M.; Branham K.E.H.; Brooks M.; Khanna R.; He S.; Lyons R.; Abecasis G.R.; Swaroop A.;
Proc. Natl. Acad. Sci. U.S.A. 104:16227-16232(2007)
Cited for: PRELIMINARY SUBCELLULAR LOCATION; TISSUE SPECIFICITY; INVOLVEMENT IN ARMD8; VARIANT SER-69;

Cigarette smoking strongly modifies the association of LOC387715 and age-related macular degeneration.
Schmidt S.; Hauser M.A.; Scott W.K.; Postel E.A.; Agarwal A.; Gallins P.; Wong F.; Chen Y.S.; Spencer K.; Schnetz-Boutaud N.; Haines J.L.; Pericak-Vance M.A.;
Am. J. Hum. Genet. 78:852-864(2006)
Cited for: INVOLVEMENT IN ARMD8; VARIANT SER-69;

CFH, ELOVL4, PLEKHA1 and LOC387715 genes and susceptibility to age-related maculopathy: AREDS and CHS cohorts and meta-analyses.
Conley Y.P.; Jakobsdottir J.; Mah T.; Weeks D.E.; Klein R.; Kuller L.; Ferrell R.E.; Gorin M.B.;
Hum. Mol. Genet. 15:3206-3218(2006)
Cited for: INVOLVEMENT IN ARMD8; VARIANT SER-69;

Common variation in three genes, including a noncoding variant in CFH, strongly influences risk of age-related macular degeneration.
Maller J.; George S.; Purcell S.; Fagerness J.; Altshuler D.; Daly M.J.; Seddon J.M.;
Nat. Genet. 38:1055-1059(2006)
Cited for: INVOLVEMENT IN ARMD8; VARIANT SER-69;

HTRA1 promoter polymorphism in wet age-related macular degeneration.
Dewan A.; Liu M.; Hartman S.; Zhang S.S.-M.; Liu D.T.L.; Zhao C.; Tam P.O.S.; Chan W.M.; Lam D.S.C.; Snyder M.; Barnstable C.; Pang C.P.; Hoh J.;
Science 314:989-992(2006)
Cited for: INVOLVEMENT IN ARMD8; VARIANT SER-69;

A prospective study of 2 major age-related macular degeneration susceptibility alleles and interactions with modifiable risk factors.
Schaumberg D.A.; Hankinson S.E.; Guo Q.; Rimm E.; Hunter D.J.;
Arch. Ophthalmol. 125:55-62(2007)
Cited for: INVOLVEMENT IN ARMD8; VARIANT SER-69;

Variants in the 10q26 gene cluster (LOC387715 and HTRA1) exhibit enhanced risk of age-related macular degeneration along with CFH in Indian patients.
Kaur I.; Katta S.; Hussain A.; Hussain N.; Mathai A.; Narayanan R.; Hussain A.; Reddy R.K.; Majji A.B.; Das T.; Chakrabarti S.;
Invest. Ophthalmol. Vis. Sci. 49:1771-1776(2008)
Cited for: INVOLVEMENT IN ARMD8; VARIANT SER-69;

Age-related macular degeneration genetics.
Recalde S.; Fernandez-Robredo P.; Altarriba M.; Salinas-Alaman A.; Garcia-Layana A.;
Ophthalmology 115:916-916(2008)
Cited for: INVOLVEMENT IN ARMD8; VARIANT SER-69;

The LOC387715 polymorphism, inflammatory markers, smoking, and age-related macular degeneration. A population-based case-control study.
Wang J.J.; Ross R.J.; Tuo J.; Burlutsky G.; Tan A.G.; Chan C.-C.; Favaloro E.J.; Williams A.; Mitchell P.;
Ophthalmology 115:693-699(2008)
Cited for: INVOLVEMENT IN ARMD8; VARIANT SER-69;

CFH and LOC387715/ARMS2 genotypes and treatment with antioxidants and zinc for age-related macular degeneration.
Klein M.L.; Francis P.J.; Rosner B.; Reynolds R.; Hamon S.C.; Schultz D.W.; Ott J.; Seddon J.M.;
Ophthalmology 115:1019-1025(2008)
Cited for: INVOLVEMENT IN ARMD8; VARIANT SER-69;

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.