chr11:6415746:G>A Detail (hg19) (SMPD1)

Information

Genome

Assembly Position
hg19 chr11:6,415,746-6,415,746
hg38 chr11:6,394,516-6,394,516 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000543.4:c.1805G>A NP_000534.3:p.Arg602His
NM_001007593.2:c.1805G>A NP_001007594.2:p.Arg602His
NM_001318087.1:c.1805G>A NP_001305016.1:p.Arg602His
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:<0.001
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:<0.001

Prediction

ClinVar

Clinical Significance Pathogenic Likely pathogenic
Review star
Show details
Links
Type Database ID Link
Gene MIM 607608 OMIM
HGNC 11120 HGNC
Ensembl ENSG00000166311 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv41492310 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Pathogenic Likely pathogenic 2023-09-20 criteria provided, multiple submitters, no conflicts Niemann-Pick disease, type A germline unknown Detail
Pathogenic 2024-01-31 criteria provided, single submitter Niemann-Pick disease, type B,Niemann-Pick disease, type A germline Detail
Pathogenic 2024-01-31 criteria provided, single submitter Niemann-Pick disease, type B,Niemann-Pick disease, type A germline Detail
Pathogenic 2022-04-14 criteria provided, multiple submitters, no conflicts Sphingomyelin/cholesterol lipidosis germline Detail
Pathogenic 2019-08-16 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.562 Niemann-Pick disease, type A NA CLINVAR Detail
0.266 Niemann-Pick Diseases For this purpose, we have used cultured Niemann-Pick disease (NPD) lymphoid cell... BeFree 9516458 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000543.5(SMPD1):c.1805G>A (p.Arg602His) AND Niemann-Pick disease, type A ClinVar Detail
NM_000543.5(SMPD1):c.1805G>A (p.Arg602His) AND multiple conditions ClinVar Detail
NM_000543.5(SMPD1):c.1805G>A (p.Arg602His) AND multiple conditions ClinVar Detail
NM_000543.5(SMPD1):c.1805G>A (p.Arg602His) AND Sphingomyelin/cholesterol lipidosis ClinVar Detail
NM_000543.5(SMPD1):c.1805G>A (p.Arg602His) AND not provided ClinVar Detail
NA DisGeNET Detail
For this purpose, we have used cultured Niemann-Pick disease (NPD) lymphoid cells with a defined mut... 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
rs370129081 dbSNP
Genome
hg19
Position
chr11:6,415,746-6,415,746
Variant Type
snv
Reference Allele
G
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))
rs370129081
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0002
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
3
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
8606
East Asian Allele Counts (ExAC)
0
East Asian Heterozygous Counts (ExAC)
0
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.0
Chromosome Counts in All Race (ExAC)
120896
Allele Counts in All Race (ExAC)
4
Heterozygous Counts in All Race (ExAC)
4
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
3.308628904182107E-5
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