rs1544410 - GET-Evidence

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rs1544410


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Short summary

rs1544410 is a Vitamin D Receptor (VDR) single nucleotide polymorphism. It is unlikely that it has functional significance because it is located in an intron (Liu et. al.), but it is in strong linkage disequilibrium with rs731236 (Dvornyk et al), which is located in an exon.

Variant evidence
Computational 1

This variant does change risk factors for Type I and Type II Diabetes rather significantly.

Functional -1

This variant is located in a non-coding region of the genome, and it is unlikely that it has functional significance.

Case/Control
Familial
 
Clinical importance
Severity 1

Associated with an elevated risk of Type II Diabetes (see explanation below).

Treatability

There are no known interventions.

Penetrance

Although this variant gives an individual an increased odds ratio for Type I Diabetes, it is likely that this is due to linkage disequilibrium with another variant rather than functional effect.

 

Impact

Low clinical importance, Uncertain pharmacogenetic

(The "low clinical importance, uncertain" qualifier is assigned automatically based on the above evidence and importance scores.)

Inheritance pattern

unknown

Summary of published research, and additional commentary

This variant has been studied extensively. It has been linked to Type II Diabetes (Mukhopadhyaya et al) and Type I Diabetes (Panierakis et al). However, these studies both linked rs731236 to the disease, and the second study linked rs731236 with a much higher odds ratio than rs1544410 (4.43 vs. 2.19) Since rs731236 is located in an exon while rs1544410 is located in an intron and the two variants are in strong linkage disequilibrium, it is likely that the functional effect seen in these studies comes from the other variant.

Since the vitamin D receptor gene has been implicated in a wide variety of diseases (diabetes, various types of cancer, etc.), its polymorphisms have been fairly intensely studied. However, rs1544410 has relatively little effect on most of these diseases, possibly due to its being located in an intron.

Dvornyk, V, JR Long, PY Liu, H Shen, RR Recker and HW Deng. “Polymorphisms of the vitamin D receptor gene predict the onset of surgical menopause in Caucasian females. .” Gynecol Endocrinol (2006): n. pag. Web. 3 Apr 2011.

Liu, Yao, Wei Chen, Zhi-bin Hu, Lin Xu, Yong-qian Shu, Shi-yang Pan Jun-Chang Dai, Guang-Fu Jin, Hong-zia Ma and Hong-bing Shen. “Plasma Vitamin D Levels And Vitamin D Receptor Polymorphisms Are Associated with Survival of Non-small Cell Lung Cancer.” Chin J Cancer Res (2011): n. pag. Web. 31 Mar 2011.

Mukhopadhyaya , P.N. , A, Acharya , Y. Chavan , S.S. Purohit , and A. Mutha. “Metagenomic study of single-nucleotide polymorphism within candidate genes associated with type 2 diabetes in an Indian population.” Genetics and Molecular Research 9.4 (2010): n. pag. Web. 3 Apr 2011.

Panierakis, Charalambos , George Goulielmos , Mamoulakis Dimitris, Eleni Petraki , Efstathios Papavasiliou, and Emmanouil Galanakis . “Vitamin D receptor gene polymorphisms and susceptibility to type 1 diabetes in Crete, Greece.” Clinical Immunology 133. (2009): n. pag. Web. 3 Apr 2011.

Allele frequency

  • T @ chr12:46526101: 35.2% (45/128) in GET-Evidence
  • Frequency shown in summary reports: 35.2% (45/128)

Publications
 

Genomes
 

hu034DB1 - CGI sample GS00253-DNA_A02_200_37
het T @ chr12:48239835

 

hu04FD18 - CGI sample GS00253-DNA_F01_200_37
het T @ chr12:48239835

 

hu0D879F - CGI sample GS00253-DNA_G01_200_37
het T @ chr12:48239835

 

Added in this revision:

hu241DEA - CGI sample GS01175-DNA_D05 from PGP sample 1205491
het T @ chr12:48239835

 

hu2D6140 - CGI sample GS01173-DNA_F06 from PGP sample 64191565
het T @ chr12:48239835

 

hu2DBF2D - CGI sample GS01173-DNA_G02 from PGP sample 67180598
hom T @ chr12:48239835

 

 

hu342A08 - CGI sample GS01175-DNA_B05 from PGP sample 83494370
hom T @ chr12:48239835

 

 

hu4339C0 - CGI sample GS01175-DNA_H01 from PGP sample 94797469
het T @ chr12:48239835

 

hu43860C - CGI sample GS00253-DNA_A01_200_37
hom T @ chr12:48239835

 

hu604D39 - CGI sample GS00253-DNA_B02_200_37
het T @ chr12:48239835

 

hu72A81D - CGI sample GS01173-DNA_C02 from PGP sample 10366372
het T @ chr12:48239835

 

hu8229AE - CGI sample GS01173-DNA_A07 from PGP sample 96240009
het T @ chr12:48239835

 

hu9385BA - CGI sample GS00253-DNA_E01_200_37
het T @ chr12:48239835

 

huA0E089 - CGI sample GS01175-DNA_B04 from PGP sample 88590671
het T @ chr12:48239835

 

huAE6220 - CGI sample GS00253-DNA_H01_200_37
het T @ chr12:48239835

 

huBEDA0B - CGI sample GS00253-DNA_C01_200_37
het T @ chr12:48239835

 

huC30901 - CGI sample GS00253-DNA_B01_200_37
het T @ chr12:48239835

 

huD81F3D - CGI sample GS01173-DNA_D06 from PGP sample 69488604
het T @ chr12:48239835

 

huE80E3D - CGI sample GS00253-DNA_D01_200_37
hom T @ chr12:48239835

 

huFAF983 - CGI sample GS01175-DNA_F02 from PGP sample 95788191
het T @ chr12:48239835

 

GS06985 - var-GS06985-1100-36-ASM
het T @ chr12:46526102

 

GS10851 - var-GS10851-1100-36-ASM
het T @ chr12:46526102

 

GS18502 - var-GS18502-1100-36-ASM
hom T @ chr12:46526102

 

GS18504 - var-GS18504-1100-36-ASM
het T @ chr12:46526102

 

GS18508 - var-GS18508-1100-36-ASM
hom T @ chr12:46526102

 

GS18517 - var-GS18517-1100-36-ASM
hom T @ chr12:46526102

 

GS18956 - var-GS18956-1100-36-ASM
het T @ chr12:46526102

 

GS19025 - var-GS19025-1100-36-ASM
het T @ chr12:46526102

 

GS19238 - var-GS19238-1100-36-ASM
het T @ chr12:46526102

 

GS19648 - var-GS19648-1100-36-ASM
het T @ chr12:46526102

 

GS19649 - var-GS19649-1100-36-ASM
het T @ chr12:46526102

 

GS19669 - var-GS19669-1100-36-ASM
het T @ chr12:46526102

 

GS19700 - var-GS19700-1100-36-ASM
het T @ chr12:46526102

 

GS19834 - var-GS19834-1100-36-ASM
het T @ chr12:46526102

 

GS20502 - var-GS20502-1100-36-ASM
het T @ chr12:46526102

 

GS20509 - var-GS20509-1100-36-ASM
het T @ chr12:46526102

 

GS21767 - var-GS21767-1100-36-ASM
het T @ chr12:46526102

 

Other external references
 

    dbSNP
  • rs1544410
    www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi

Other in silico analyses
 

  • GET-Evidence autoscore = 1

Edit history
 

Gene search

"GENE" or "GENE A123C":

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