chr18:21140432:T>C Detail (hg19) (NPC1)

Information

Genome

Assembly Position
hg19 chr18:21,140,432-21,140,432
hg38 chr18:23,560,468-23,560,468 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000271.4:c.644A>G NP_000262.2:p.His215Arg
Ensemble ENST00000269228.10:c.644A>G ENST00000269228.10:p.His215Arg
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.268
ToMMo:0.283
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.238

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 607623 OMIM
HGNC 7897 HGNC
Ensembl ENSG00000141458 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv59424315 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2016-03-28 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2024-02-01 criteria provided, multiple submitters, no conflicts Niemann-Pick disease, type C1 germline Detail
Benign 2015-10-21 no assertion criteria provided not provided unknown Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.251 obesity Most notably, the association between 5 SNPs (Fas apoptotic inhibitory molecule ... BeFree 21527513 Detail
0.791 obesity Most notably, the association between 5 SNPs (Fas apoptotic inhibitory molecule ... BeFree 21527513 Detail
0.159 obesity Most notably, the association between 5 SNPs (Fas apoptotic inhibitory molecule ... BeFree 21527513 Detail
0.400 obesity Most notably, the association between 5 SNPs (Fas apoptotic inhibitory molecule ... BeFree 21527513 Detail
0.001 obesity The NPC1 variant rs1805081 showed some evidence of association with %BF (β=0.013... BeFree 22430306 Detail
0.251 obesity A polymorphism (His215Arg) in NPC1 was associated with obesity in Europeans. BeFree 23153210 Detail
0.251 obesity In addition to FTO and MC4R, we detected significant association of obesity with... GWASCAT 19151714 Detail
0.251 obesity [In addition to FTO and MC4R, we detected significant association of obesity wit... GAD 19151714 Detail
0.005 obesity In each study, we tested associations of rs4712652 (near-PRL), rs10508503 (near-... BeFree 22430306 Detail
<0.001 Overweight In each study, we tested associations of rs4712652 (near-PRL), rs10508503 (near-... BeFree 22430306 Detail
<0.001 Hypertensive disease Of the 11 SNPs, only FTO rs9939609 was significantly associated with systolic BP... BeFree 23588626 Detail
<0.001 Hypertensive disease Of the 11 SNPs, only FTO rs9939609 was significantly associated with systolic BP... BeFree 23588626 Detail
0.153 obesity Among those previously identified SNPs, we selected six (rs7138803, rs1805081, r... BeFree 20843981 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000271.5(NPC1):c.644A>G (p.His215Arg) AND not specified ClinVar Detail
NM_000271.5(NPC1):c.644A>G (p.His215Arg) AND Niemann-Pick disease, type C1 ClinVar Detail
NM_000271.5(NPC1):c.644A>G (p.His215Arg) AND not provided ClinVar Detail
Most notably, the association between 5 SNPs (Fas apoptotic inhibitory molecule 2 rs7138803, Niemann... DisGeNET Detail
Most notably, the association between 5 SNPs (Fas apoptotic inhibitory molecule 2 rs7138803, Niemann... DisGeNET Detail
Most notably, the association between 5 SNPs (Fas apoptotic inhibitory molecule 2 rs7138803, Niemann... DisGeNET Detail
Most notably, the association between 5 SNPs (Fas apoptotic inhibitory molecule 2 rs7138803, Niemann... DisGeNET Detail
The NPC1 variant rs1805081 showed some evidence of association with %BF (β=0.013 s.d./allele, P=0.04... DisGeNET Detail
A polymorphism (His215Arg) in NPC1 was associated with obesity in Europeans. DisGeNET Detail
In addition to FTO and MC4R, we detected significant association of obesity with three new risk loci... DisGeNET Detail
[In addition to FTO and MC4R, we detected significant association of obesity with three new risk loc... DisGeNET Detail
In each study, we tested associations of rs4712652 (near-PRL), rs10508503 (near-PTER), rs1424233 (ne... DisGeNET Detail
In each study, we tested associations of rs4712652 (near-PRL), rs10508503 (near-PTER), rs1424233 (ne... DisGeNET Detail
Of the 11 SNPs, only FTO rs9939609 was significantly associated with systolic BP (SBP; P=0.034) and ... DisGeNET Detail
Of the 11 SNPs, only FTO rs9939609 was significantly associated with systolic BP (SBP; P=0.034) and ... DisGeNET Detail
Among those previously identified SNPs, we selected six (rs7138803, rs1805081, rs6499640, rs17782313... DisGeNET Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs1805081 dbSNP
Genome
hg19
Position
chr18:21,140,432-21,140,432
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1206
Mean of sample read depth (HGVD)
56.42
Standard deviation of sample read depth (HGVD)
24.98
Number of reference allele (HGVD)
1766
Number of alternative allele (HGVD)
646
Allele Frequency (HGVD)
0.2678275290215589
Gene Symbol (HGVD)
NPC1
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))
rs1805081
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.2829
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
4742
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8590
East Asian Allele Counts (ExAC)
2048
East Asian Heterozygous Counts (ExAC)
1600
East Asian Homozygous Counts (ExAC)
224
East Asian Allele Frequency (ExAC)
0.23841676367869616
Chromosome Counts in All Race (ExAC)
120438
Allele Counts in All Race (ExAC)
39592
Heterozygous Counts in All Race (ExAC)
25034
Homozygous Counts in All Race (ExAC)
7279
Allele Frequency in All Race (ExAC)
0.32873345621813715
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