ITGAM R77H - 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.

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Curation:
Currentness:

ITGAM R77H

(ITGAM Arg77His)


Short summary

 

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

  • A @ chr16:31276811: 10.5% (1085/10304) in EVS
  • A @ chr16:31184311: 9.5% (12/126) in GET-Evidence
  • Frequency shown in summary reports: 10.5% (1085/10304)

Publications
 

Nath SK, Han S, Kim-Howard X, Kelly JA, Viswanathan P, Gilkeson GS, Chen W, Zhu C, McEver RP, Kimberly RP, Alarcón-Riquelme ME, Vyse TJ, Li QZ, Wakeland EK, Merrill JT, James JA, Kaufman KM, Guthridge JM, Harley JB. A nonsynonymous functional variant in integrin-alpha(M) (encoded by ITGAM) is associated with systemic lupus erythematosus. Nat Genet. 2008 Feb;40(2):152-4. Epub 2008 Jan 20. PubMed PMID: 18204448.

 

Genomes
 

hu025CEA - CGI sample GS01669-DNA_D02 from PGP sample 27316983
het A @ chr16:31276811

 

hu0D879F - CGI sample GS00253-DNA_G01_200_37
het A @ chr16:31276811

 

hu2D6140 - CGI sample GS01173-DNA_F06 from PGP sample 64191565
het A @ chr16:31276811

 

 

 

hu43860C

 

hu72A81D - CGI sample GS01173-DNA_C02 from PGP sample 10366372
het A @ chr16:31276811

 

hu9385BA - CGI sample GS00253-DNA_E01_200_37
het A @ chr16:31276811

 

huB1FD55 - CGI sample GS01173-DNA_B07 from PGP sample 61499538
het A @ chr16:31276811

 

huC30901 - CGI sample GS00253-DNA_B01_200_37
het A @ chr16:31276811

 

huD37D14 - CGI sample GS01175-DNA_A04 from PGP sample 13272228
het A @ chr16:31276811

 

huD81F3D - CGI sample GS01173-DNA_D06 from PGP sample 69488604
het A @ chr16:31276811

 

huE80E3D - CGI sample GS00253-DNA_D01_200_37
het A @ chr16:31276811

 

GS18501 - var-GS18501-1100-36-ASM
het A @ chr16:31184312

 

GS19020 - var-GS19020-1100-36-ASM
het A @ chr16:31184312

 

GS19026 - var-GS19026-1100-36-ASM
het A @ chr16:31184312

 

GS20502 - var-GS20502-1100-36-ASM
het A @ chr16:31184312

 

GS20509 - var-GS20509-1100-36-ASM
het A @ chr16:31184312

 

Other external references
 

    dbSNP
  • rs1143679
    www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi
    PharmGKB
  • [Lupus Erythematosus, Systemic]
    This nonsynonymous SNP is an associated with risk of systemic lupus erythematosus in a study with 3,818 individuals of European descent.
    www.ncbi.nlm.nih.gov/pubmed/18204448
    PolyPhen-2
  • Score: 0.048 (benign)

Other in silico analyses
 

  • NBLOSUM100 score = 1
  • GET-Evidence autoscore = 2

Edit history
 

Gene search

"GENE" or "GENE A123C":

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