ARMS2 A69S - GET-Evidence

Note: This variant has not been sufficiently evaluated by a GET-Evidence editor.

To be considered sufficiently evaluated a variant must have both "variant evidence" and "clinical importance" scores filled in.

Please help improve GET-Evidence by evaluating evidence for this variant!

Curation:
Currentness:

ARMS2 A69S

(ARMS2 Ala69Ser)


Short summary

associated wuth polypoidal choroidal vasculopathy (PCV) and age-related macular degeneration (AMD)

Variant evidence
Computational 1

PolyPhen2: Benign, score 0.138
SIFT: Affect protein function 0.00
GVGD: GV 0.00; GD 99.13; Class C65
Variant Effect Predictor (Ensembl):
PolyPhen=benign(0.138)

Functional -
Case/Control 3

See Chen H et al. 2012 (22509112), Kenney MC et al. 2013 (23302509).

Familial -
 
Clinical importance
Severity 2

See Kenney MC et al. 2013 (23302509).

Treatability -
Penetrance -
 

Impact

Insufficiently evaluated pathogenic

(The "insufficiently evaluated" qualifier is assigned automatically based on the above evidence and importance scores.)

Inheritance pattern

unknown

Summary of published research, and additional commentary

 

Allele frequency

  • T @ chr10:124214448: 20.7% (2100/10124) in EVS
  • T @ chr10:124204437: 28.1% (36/128) in GET-Evidence
  • Frequency shown in summary reports: 20.7% (2100/10124)

Publications
 

Yang Z, Camp NJ, Sun H, Tong Z, Gibbs D, Cameron DJ, Chen H, Zhao Y, Pearson E, Li X, Chien J, Dewan A, Harmon J, Bernstein PS, Shridhar V, Zabriskie NA, Hoh J, Howes K, Zhang K. A variant of the HTRA1 gene increases susceptibility to age-related macular degeneration. Science. 2006 Nov 10;314(5801):992-3. Epub 2006 Oct 19. PubMed PMID: 17053109.

 

Chen H, Liu K, Chen LJ, Hou P, Chen W, Pang CP. Genetic associations in polypoidal choroidal vasculopathy: a systematic review and meta-analysis. Mol Vis. 2012;18:816-29. Epub 2012 Apr 4. Review. PubMed PMID: 22509112; PubMed Central PMCID: PMC3324368.

 

Kenney MC, Hertzog D, Chak G, Atilano SR, Khatibi N, Soe K, Nobe A, Yang E, Chwa M, Zhu F, Memarzadeh M, King J, Langberg J, Small K, Nesburn AB, Boyer DS, Udar N. Mitochondrial DNA haplogroups confer differences in risk for age-related macular degeneration: a case control study. BMC Med Genet. 2013 Jan 9;14(1):4. [Epub ahead of print] PubMed PMID: 23302509.

 

Genomes
 

hu034DB1 - CGI sample GS00253-DNA_A02_200_37
het T @ chr10:124214448

 

hu0D879F - CGI sample GS00253-DNA_G01_200_37
hom T @ chr10:124214448

 

 

hu2DBF2D - CGI sample GS01173-DNA_G02 from PGP sample 67180598
het T @ chr10:124214448

 

 

hu3CAB43 - CGI sample GS01175-DNA_D03 from PGP sample 27486199
het T @ chr10:124214448

 

hu4339C0 - CGI sample GS01175-DNA_H01 from PGP sample 94797469
het T @ chr10:124214448

 

hu43860C - CGI sample GS00253-DNA_A01_200_37
het T @ chr10:124214448

 

hu4CA5B9 - CGI sample GS01669-DNA_B03 from PGP sample 14427241
hom T @ chr10:124214448

 

hu604D39 - CGI sample GS00253-DNA_B02_200_37
hom T @ chr10:124214448

 

 

 

hu72A81D - CGI sample GS01173-DNA_C02 from PGP sample 10366372
hom T @ chr10:124214448

 

hu8229AE - CGI sample GS01173-DNA_A07 from PGP sample 96240009
het T @ chr10:124214448

 

hu92C40A - CGI sample GS01175-DNA_G03 from PGP sample 92527586
het T @ chr10:124214448

 

hu92FD55 - CGI sample GS01669-DNA_A04 from PGP sample 08188426
het T @ chr10:124214448

 

hu9385BA - CGI sample GS00253-DNA_E01_200_37
het T @ chr10:124214448

 

huAE4A11 - CGI sample GS01669-DNA_F02 from PGP sample 40767107
het T @ chr10:124214448

 

huC30901 - CGI sample GS00253-DNA_B01_200_37
het T @ chr10:124214448

 

huD37D14 - CGI sample GS01175-DNA_A04 from PGP sample 13272228
het T @ chr10:124214448

 

huFFAD87 - CGI sample GS01669-DNA_H05 from PGP sample 10971581
hom T @ chr10:124214448

 

GS12004 - var-GS12004-1100-36-ASM
het T @ chr10:124204438

 

GS18501 - var-GS18501-1100-36-ASM
het T @ chr10:124204438

 

GS18537 - var-GS18537-1100-36-ASM
het T @ chr10:124204438

 

GS18555 - var-GS18555-1100-36-ASM
het T @ chr10:124204438

 

GS18558 - var-GS18558-1100-36-ASM
hom T @ chr10:124204438

 

GS18942 - var-GS18942-1100-36-ASM
het T @ chr10:124204438

 

GS18956 - var-GS18956-1100-36-ASM
het T @ chr10:124204438

 

GS19025 - var-GS19025-1100-36-ASM
het T @ chr10:124204438

 

GS19129 - var-GS19129-1100-36-ASM
het T @ chr10:124204438

 

GS19239 - var-GS19239-1100-36-ASM
het T @ chr10:124204438

 

GS19649 - var-GS19649-1100-36-ASM
het T @ chr10:124204438

 

GS19670 - var-GS19670-1100-36-ASM
het T @ chr10:124204438

 

GS19700 - var-GS19700-1100-36-ASM
het T @ chr10:124204438

 

GS19701 - var-GS19701-1100-36-ASM
het T @ chr10:124204438

 

GS19703 - var-GS19703-1100-36-ASM
het T @ chr10:124204438

 

GS19704 - var-GS19704-1100-36-ASM
hom T @ chr10:124204438

 

Other external references
 

    dbSNP
  • rs10490924
    www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi
    PharmGKB
  • [Macular Degeneration]
    In confirmation of other studies, rs10490924 was found to be significantly associated with risk of Age-related Macular degeneration in a Caucasian (White) case-control study.
    www.ncbi.nlm.nih.gov/pubmed/17053109

Other in silico analyses
 

  • NBLOSUM100 score = –1
  • GET-Evidence autoscore = 3

Edit history
 

Gene search

"GENE" or "GENE A123C":

Log in