chr5:1342714:C>A Detail (hg19) (CLPTM1L)

Information

Genome

Assembly Position
hg19 chr5:1,342,714-1,342,714
hg38 chr5:1,342,599-1,342,599 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_030782.4:c.264-739G>T
Ensemble ENST00000320895.10:c.264-739G>T
ENST00000630539.1:c.-136-739G>T
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.130
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 612585 OMIM
HGNC 24308 HGNC
Ensembl ENSG00000049656 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv20014065 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 nicotine dependence Gene variations rs2736100 and rs2853676 in TERT and rs401681 and rs31489 in CLPT... BeFree 25233467 Detail
0.243 Adenocarcinoma of lung (disorder) Gene variations rs2736100 and rs2853676 in TERT and rs401681 and rs31489 in CLPT... BeFree 25233467 Detail
<0.001 Malignant neoplasm of lung Cleft lip and palate transmembrane protein 1 rs31489 polymorphism is associated ... BeFree 24535780 Detail
0.243 Adenocarcinoma of lung (disorder) A genome-wide association study of lung cancer identifies a region of chromosome... GWASCAT 19836008 Detail
0.005 Pancreatic Neoplasm NA GAD Detail
0.135 Lung Neoplasms [, a lung cancer GWAS identified a distinct hereditary contribution to adenocarc... GAD 19836008 Detail
0.143 Malignant neoplasm of lung In conclusion, this meta-analysis suggested that CLPTM1L rs31489 was a potential... BeFree 24535780 Detail
0.009 Carcinoma of lung In conclusion, this meta-analysis suggested that CLPTM1L rs31489 was a potential... BeFree 24535780 Detail
<0.001 Carcinoma of lung Cleft lip and palate transmembrane protein 1 rs31489 polymorphism is associated ... BeFree 24535780 Detail
0.243 Adenocarcinoma of lung (disorder) [a lung cancer GWAS identified a distinct hereditary contribution to adenocarcin... GAD 19836008 Detail
Annotation

Annotations

DescrptionSourceLinks
Gene variations rs2736100 and rs2853676 in TERT and rs401681 and rs31489 in CLPTM1L had significant ... DisGeNET Detail
Gene variations rs2736100 and rs2853676 in TERT and rs401681 and rs31489 in CLPTM1L had significant ... DisGeNET Detail
Cleft lip and palate transmembrane protein 1 rs31489 polymorphism is associated with lung cancer ris... DisGeNET Detail
A genome-wide association study of lung cancer identifies a region of chromosome 5p15 associated wit... DisGeNET Detail
NA DisGeNET Detail
[, a lung cancer GWAS identified a distinct hereditary contribution to adenocarcinoma.] DisGeNET Detail
In conclusion, this meta-analysis suggested that CLPTM1L rs31489 was a potential biomarker for lung ... DisGeNET Detail
In conclusion, this meta-analysis suggested that CLPTM1L rs31489 was a potential biomarker for lung ... DisGeNET Detail
Cleft lip and palate transmembrane protein 1 rs31489 polymorphism is associated with lung cancer ris... DisGeNET Detail
[a lung cancer GWAS identified a distinct hereditary contribution to adenocarcinoma.] DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs31489 dbSNP
Genome
hg19
Position
chr5:1,342,714-1,342,714
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))
rs31489
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1303
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
2184
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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