PECAM1 L125V

(PECAM1 Leu125Val)

Mismatched genotypes in this variant between donor and recipient is associated with causing graft vs. host disease in bone marrow transplants.

Variant evidence
Computational	1	An adhesion molecule on the cell surface, may be recognized as an antigen

Functional

Case/Control	4	p = 0.004 See Behar E et al. 1996 (8532023).
		p = 0.004 See Behar E et al. 1996 (8532023).
Familial


Clinical importance
Severity	3	acute graft vs. host disease
		acute graft vs. host disease
Treatability	4	Avoiding mismatched genotypes addresses this issue, but may not be possible

Penetrance	1	We estimate it increases chances of GVHD by 25-30%, but GVHD is a rare condition as most individuals do not get bone marrow transplants.

Low clinical importance, Likely pharmacogenetic

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

other

We mark this as pharmacogenetic because it is normally benign, but could be pathogenic in the context of medical treatment — i.e. it might affect the type of medical treatment an individual would receive.

Assuming a GVHD rate of 30% in HLA matched siblings, the mismatched PECAM genotypes have a risk of ~58%, an attributable increased risk of ~28%.

Allele frequency

C @ chr17:59804698: 57.0% (73/128) in GET-Evidence
Frequency shown in summary reports: 57.0% (73/128)

Publications

CD31 genotyping of 46 recipients of bone marrow: 14 with severe graph vs. host disease (GVHD) and 32 without GVHD, along with donor genotyping. 10 of the 14 recipients that had acute GVHD did not match donor genotype (HLA-matched siblings), while only 7 of the 32 without GVHD had a mismatch. The authors report p = 0.004, we calculate 0.0024 with two-tailed Fisher’s Exact.

Genomes

Other external references

dbSNP

rs668
www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi

OMIM

Platelet-endothelial cell adhesion molecule 1 polymorphism
www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=173445

PolyPhen-2

Score: 0 (benign)

Other in silico analyses

NBLOSUM100 score = 0
GET-Evidence autoscore = 2

Edit history

Mar 5 2012 Genome Importing Robot added hu232307 build 36 substitution variants view
Jun 23 2011 Genome Importing Robot removed James D. Watson view
Jun 23 2011 Genome Importing Robot removed [NA18507] view
Jun 23 2011 Genome Importing Robot removed [NA07022] view
Jun 22 2011 Genome Importing Robot removed J. Craig Venter view
Jun 22 2011 Genome Importing Robot removed [NA19240] view
Jun 22 2011 Genome Importing Robot removed [snp-3] view
Jun 22 2011 Genome Importing Robot removed !Gubi view
Jun 22 2011 Genome Importing Robot removed Desmond Tutu view
Jun 22 2011 Genome Importing Robot removed [snp-2] view
Jun 22 2011 Genome Importing Robot removed Seong-Jin Kim view
May 20 2011 Madeleine Ball edited variant summary view
Mar 29 2011 Genome Importing Robot added var-GS21767-1100-36-ASM view
Mar 29 2011 Genome Importing Robot added var-GS20509-1100-36-ASM view
Mar 29 2011 Genome Importing Robot added var-GS20502-1100-36-ASM view
Mar 29 2011 Genome Importing Robot added var-GS19834-1100-36-ASM view
Mar 29 2011 Genome Importing Robot added var-GS19704-1100-36-ASM view
Mar 29 2011 Genome Importing Robot added var-GS19703-1100-36-ASM view
Mar 29 2011 Genome Importing Robot added var-GS19701-1100-36-ASM view
Mar 29 2011 Genome Importing Robot added var-GS19700-1100-36-ASM view
Mar 29 2011 Genome Importing Robot added var-GS19670-1100-36-ASM view
Mar 29 2011 Genome Importing Robot added var-GS19649-1100-36-ASM view
Mar 29 2011 Genome Importing Robot added var-GS19648-1100-36-ASM view
Mar 29 2011 Genome Importing Robot added var-GS19240-1100-36-ASM view
Mar 29 2011 Genome Importing Robot added var-GS19239-1100-36-ASM view
Mar 29 2011 Genome Importing Robot added var-GS19238-1100-36-ASM view
Mar 29 2011 Genome Importing Robot added var-GS19129-1100-36-ASM view
Mar 29 2011 Genome Importing Robot added var-GS19026-1100-36-ASM view
Mar 29 2011 Genome Importing Robot added var-GS19020-1100-36-ASM view
Mar 29 2011 Genome Importing Robot added var-GS19017-1100-36-ASM view
Mar 29 2011 Genome Importing Robot added var-GS18956-1100-36-ASM view
Mar 29 2011 Genome Importing Robot added var-GS18947-1100-36-ASM view
Mar 29 2011 Genome Importing Robot added var-GS18942-1100-36-ASM view
Mar 29 2011 Genome Importing Robot added var-GS18940-1100-36-ASM view
Mar 29 2011 Genome Importing Robot added var-GS18558-1100-36-ASM view
Mar 29 2011 Genome Importing Robot added var-GS18537-1100-36-ASM view
Mar 29 2011 Genome Importing Robot added var-GS18526-1100-36-ASM view
Mar 29 2011 Genome Importing Robot added var-GS18517-1100-36-ASM view
Mar 29 2011 Genome Importing Robot added var-GS18508-1100-36-ASM view
Mar 29 2011 Genome Importing Robot added var-GS06994-1100-36-ASM view
Mar 29 2011 Genome Importing Robot added var-GS10851-1100-36-ASM view
Mar 29 2011 Genome Importing Robot added var-GS18501-1100-36-ASM view
Mar 29 2011 Genome Importing Robot added var-GS07357-1100-36-ASM view
Mar 29 2011 Genome Importing Robot added var-GS12004-1100-36-ASM view
Mar 29 2011 Genome Importing Robot added var-GS18502-1100-36-ASM view
Mar 29 2011 Genome Importing Robot added var-GS18504-1100-36-ASM view
Mar 29 2011 Genome Importing Robot added var-GS18505-1100-36-ASM view
Dec 8 2010 Genome Importing Robot removed Henry Louis Gates Jr. view
Dec 8 2010 Genome Importing Robot removed Henry Louis Gates Sr. view
Dec 6 2010 Genome Importing Robot added hu3215A7 build 36 substitution variants view
Dec 6 2010 Genome Importing Robot added hu728FFF build 36 substitution variants view
Dec 5 2010 Genome Importing Robot added CGI sample GS00253-DNA_B02_200_37 view
Dec 5 2010 Genome Importing Robot added CGI sample GS00253-DNA_H01_200_37 view
Dec 5 2010 Genome Importing Robot added CGI sample GS00253-DNA_G01_200_37 view
Dec 5 2010 Genome Importing Robot added CGI sample GS00253-DNA_E01_200_37 view
Dec 5 2010 Genome Importing Robot added CGI sample GS00253-DNA_C01_200_37 view
Dec 5 2010 Genome Importing Robot added CGI sample GS00253-DNA_B01_200_37 view
Nov 29 2010 Leon Peshkin edited article 8532023 summary view
Nov 29 2010 Leon Peshkin edited variant summary view
Nov 29 2010 Leon Peshkin edited article 8532023 summary view
Nov 29 2010 Leon Peshkin edited variant summary view
Nov 17 2010 Madeleine Ball edited variant summary view
Nov 16 2010 Madeleine Ball edited variant summary view
Nov 16 2010 Madeleine Ball edited variant summary view
Nov 16 2010 Madeleine Ball edited variant summary view
Nov 16 2010 Madeleine Ball edited article 8532023 summary view
May 12 2010 Genome Importing Robot added Henry Louis Gates Jr. view
May 8 2010 Genome Importing Robot added [NA19240] view
Mar 5 2010 Madeleine Ball edited variant summary view
Mar 2 2010 Madeleine Ball edited variant summary view
Feb 27 2010 Genome Importing Robot added !Gubi view
Feb 27 2010 Genome Importing Robot added Desmond Tutu view
Feb 26 2010 Madeleine Ball edited variant summary view
Feb 17 2010 Genome Importing Robot added Henry Louis Gates Sr. view
Feb 12 2010 Abraham Rosenbaum edited variant summary view
Feb 12 2010 Abraham Rosenbaum edited variant summary view
Feb 12 2010 Abraham Rosenbaum edited article 8532023 summary view
Feb 12 2010 Abraham Rosenbaum added article 8532023 view
Jan 5 2010 OMIM Importing Robot edited variant summary view
Dec 27 2009 Genome Importing Robot added CGI sample GS00253-DNA_A01_200_37 view
Dec 27 2009 Genome Importing Robot added [NA07022] view
Dec 27 2009 Genome Importing Robot added J. Craig Venter view
Dec 27 2009 Genome Importing Robot added [NA18507] view
Dec 27 2009 Genome Importing Robot added [snp-3] view
Dec 27 2009 Genome Importing Robot added [snp-2] view
Dec 27 2009 Genome Importing Robot added James D. Watson view
Dec 27 2009 Genome Importing Robot added Seong-Jin Kim view
Dec 27 2009 Genome Importing Robot added variant view

PECAM1 L125V - GET-Evidence