ABCA4 R212H - GET-Evidence

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Curation:
Currentness:

ABCA4 R212H

(ABCA4 Arg212His)


Short summary

This variant has been associated with AMD.

Variant evidence
Computational -
Functional -
Case/Control -
Familial -
 
Clinical importance
Severity -
Treatability -
Penetrance -
 

Impact

Insufficiently evaluated not reviewed

(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

Using the 1000 genomes as controls (which is a difficulty assertion in a late-onset widespread disease like AMD) the OR drops to 0.22

Unpublished cases/controls case+ case– control+ control– p-value odds ratio
Age-related macular degeneration
- - 26 738 - -

 

Total cases/controls case+ case– control+ control– p-value odds ratio
Age-related macular degeneration
1 111 26 832 0.3532 0.288

 

Allele frequency

  • T @ chr1:94564483: 4.6% (497/10758) in EVS
  • T @ chr1:94337070: 5.5% (7/128) in GET-Evidence
  • Frequency shown in summary reports: 4.6% (497/10758)

Publications
 

Pang CP, Lam DS. Differential occurrence of mutations causative of eye diseases in the Chinese population. Hum Mutat. 2002 Mar;19(3):189-208. Review. PubMed PMID: 11857735.

This variant is seen heterozygously in a screen of 112 Chinese individuals with age-related macular degeneration. It was not seen in 94 controls.

Cases/controls case+ case– control+ control– p-value odds ratio
Age-related macular degeneration
1 111 0 94 1.0000

 

Baum L, Chan WM, Li WY, Lam DS, Wang PB, Pang CP. ABCA4 sequence variants in Chinese patients with age-related macular degeneration or Stargardt's disease. Ophthalmologica. 2003 Mar-Apr;217(2):111-4. PubMed PMID: 12592048.

The variant is seen in controls and the authors hypothesize that it has some effect on AMD.

Genomes
 

hu034DB1 - CGI sample GS00253-DNA_A02_200_37
het T @ chr1:94564483

 

 

huE80E3D - CGI sample GS00253-DNA_D01_200_37
het T @ chr1:94564483

 

 

GS19025 - var-GS19025-1100-36-ASM
het T @ chr1:94337071

 

GS19239 - var-GS19239-1100-36-ASM
het T @ chr1:94337071

 

GS19240 - var-GS19240-1100-36-ASM
het T @ chr1:94337071

 

GS21767 - var-GS21767-1100-36-ASM
het T @ chr1:94337071

 

NA12878

 

Other external references
 

    dbSNP
  • rs6657239
    www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi
    GeneTests
  • GeneTests records for the ABCA4 gene
    Age-related macular degeneration
    ABCA4-Related Retinitis Pigmentosa
    ABCA4-Related Stargardt Disease 1
    Age-Related Macular Degeneration 2
    Cone-Rod Dystrophy, Type 3
    Retinitis Pigmentosa, Autosomal Recessive
    Stargardt Disease, Autosomal Recessive
    www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/ABCA4
    PolyPhen-2
  • Score: 0.999 (probably damaging)
    Web search results (22 hits -- see all)
  • ABCA4 sequence variants in Chinese patients with age-related ...
    ABCA4 sequence variants in Chinese patients with age-related macular degeneration or ... Sequence alterations R212H, T1428M, V1433I, T1572M, I2166M, IVS6-5T>G ...
    www.ncbi.nlm.nih.gov/pubmed/12592048
  • <i>ABCA4</i> Sequence Variants in Chinese Patients with Age ...
    ABCA4 gene sequence alterations cause Stargardt's disease (STGD) and may cause some age ... Sequence alterations R212H, T1428M, V1433I, T1572M, I2166M, IVS6-5T>G ...
    content.karger.com/ProdukteDB/produkte.asp?Doi=68553
  • Denaturing HPLC Profiling of the ABCA4 Gene for Reliable ...
    scanning of the ABCA4 gene cumbersome, we describes. here the first use of denaturing HPLC ... ABCA4 gene to assess the sensitivity and the efficiency of ...
    www.clinchem.org/cgi/reprint/clinchem.2004.033241v1.pdf
  • Gendia | Microarray Testing
    gendia is an international network consisting of more than 100 laboratories. Gendia currently offers close to 2000 genetic tests.
    www.gendia.net/t18_note1.html
  • A Comprehensive Survey of Sequence Variation in the ABCA4 ...
    (ABCA4). We have studied 144 patients with STGD and 220 unaffected individuals ascertained ... the proposed role for ABCA4 in age-related macular degeneration ...
    sciencedirect.com/science?_ob=MImg&...&ie=/sdarticle.pdf
  • Retina International's Scientific Newsletter - ABCR Mutations
    (ABCR, ABCA4) Here we report a collection of currently published ABCR/ABCA4 mutations. ... At least it appears that ABCR/ABCA4 is a factor involved in AMD. ...
    www.retina-international.com/sci-news/abcrmut.htm
  • v13a221-rosenberg.hsm
    p{ABCA4 encodes a retinal specific ATP-binding transporter protein located at ... The ABCA4 protein facilitates the transport of the intradiscal photobleached ...
    www.molvis.org/molvis/v13/v13a221-rosenberg.hsm
  • usher syndrome Development of a genotyping Microarray for
    mutation analysis of the ABCA4 gene, in patients with either autosomal recessive ... analysis of the ABCA4 (ABCR) gene in autosomal recessive cone-rod dystrophy ...
    jmg.bmj.com/content/early/2006/.../jmg.2006.044784.full.pdf
  • 2 0 0 2 2 0 0 2
    ... mutation detection in the ABCA4 gene involved in Stargardt disease ... L1970F, R212C, R212H, R1108C and E471K mutations. Fetal DNA in maternal plasma: physiological aspects of ...
    www.sanraffaele.org/Upload/S/SciRep2002.PDF
  • Type II- 95%
    ... 14702039 12324459 11923287 MYO7A Q13402 R212H 210 VAR_009319 PKC (0.749) USH1B, ... ABCA4 P78363 L686S 692 VAR_012530 PIKK (0.530) STGD1 11385708 ABCA4 P78363 ...
    nih.go.kr/phosphovariant/html/family_whole/TypeII-_95.txt

Other in silico analyses
 

  • NBLOSUM100 score = 1
  • GET-Evidence autoscore = 4

Edit history
 

Gene search

"GENE" or "GENE A123C":

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