chr3:188394766:C>A Detail (hg38) (LPP)

Information

Genome

Assembly Position
hg19 chr3:188,112,554-188,112,554 View the variant detail on this assembly version.
hg38 chr3:188,394,766-188,394,766

HGVS

Type Transcript Protein
RefSeq NM_001167671.2:c.-9-11346C>A
NM_001167672.2:c.-9-11346C>A
Ensemble ENST00000414139.6:c.-9-11346C>A
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.542
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:[No Data.]

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 600700 OMIM
HGNC 6679 HGNC
Ensembl ENSG00000145012 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv15485668 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
[No Data.]
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 Ichthyosis bullosa of Siemens Additionally, three SNPs in immune-related genes (rs1464510-LPP, rs1881457-IL13,... BeFree 24041540 Detail
<0.001 juvenile rheumatoid arthritis One SNP in the LPP gene, rs1464510, showed significant association with JIA (p(t... BeFree 20647273 Detail
<0.001 irritable bowel syndrome Additionally, three SNPs in immune-related genes (rs1464510-LPP, rs1881457-IL13,... BeFree 24041540 Detail
0.130 celiac disease Newly identified genetic risk variants for celiac disease related to the immune ... GWASCAT 18311140 Detail
0.130 celiac disease [Newly identified genetic risk variants for celiac disease related to the immune... GAD 18311140 Detail
0.130 celiac disease Multiple common variants for celiac disease influencing immune gene expression. GWASCAT 20190752 Detail
0.130 celiac disease [Multiple common variants for celiac disease influencing immune gene expression.... GAD 20190752 Detail
0.123 Juvenile arthritis One SNP in the LPP gene, rs1464510, showed significant association with JIA (p(t... BeFree 20647273 Detail
0.122 vitiligo [We observed associations between generalized vitiligo and markers implicating m... GAD 20410501 Detail
0.122 vitiligo Variant of TYR and autoimmunity susceptibility loci in generalized vitiligo. GWASCAT 20410501 Detail
Annotation

Annotations

DescrptionSourceLinks
Additionally, three SNPs in immune-related genes (rs1464510-LPP, rs1881457-IL13, rs2104286-IL2RA), o... DisGeNET Detail
One SNP in the LPP gene, rs1464510, showed significant association with JIA (p(trend)=0.002, OR=1.18... DisGeNET Detail
Additionally, three SNPs in immune-related genes (rs1464510-LPP, rs1881457-IL13, rs2104286-IL2RA), o... DisGeNET Detail
Newly identified genetic risk variants for celiac disease related to the immune response. DisGeNET Detail
[Newly identified genetic risk variants for celiac disease related to the immune response.] DisGeNET Detail
Multiple common variants for celiac disease influencing immune gene expression. DisGeNET Detail
[Multiple common variants for celiac disease influencing immune gene expression.] DisGeNET Detail
One SNP in the LPP gene, rs1464510, showed significant association with JIA (p(trend)=0.002, OR=1.18... DisGeNET Detail
[We observed associations between generalized vitiligo and markers implicating multiple genes, some ... DisGeNET Detail
Variant of TYR and autoimmunity susceptibility loci in generalized vitiligo. DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs1464510 dbSNP
Genome
hg38
Position
chr3:188,394,766-188,394,766
Variant Type
snv
Reference Allele
C
Alternative Allele
A
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs1464510
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.5418
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
9080
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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