chr17:5485367:A>T Detail (hg19) (NLRP1)

Information

Genome

Assembly Position
hg19 chr17:5,485,367-5,485,367
hg38 chr17:5,582,047-5,582,047 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001033053.2:c.464T>A NP_001028225.1:p.Leu155His
NM_033004.3:c.464T>A NP_127497.1:p.Leu155His
NM_014922.4:c.464T>A NP_055737.1:p.Leu155His
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.042
ToMMo:0.039
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.035

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 606636 OMIM
HGNC 14374 HGNC
Ensembl ENSG00000091592 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv56878843 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
risk factor 2007-03-22 no assertion criteria provided Vitiligo-associated multiple autoimmune disease susceptibility 1 germline Detail
Benign 2024-02-01 criteria provided, single submitter not provided germline Detail
Benign 2021-09-05 criteria provided, single submitter Corneal intraepithelial dyskeratosis-palmoplantar hyperkeratosis-laryngeal dyskeratosis syndrome germline Detail
Benign 2021-09-05 criteria provided, single submitter Autoinflammation with arthritis and dyskeratosis germline Detail
Benign 2021-09-05 criteria provided, single submitter Respiratory papillomatosis, juvenile recurrent, congenital germline Detail
Benign 2023-11-12 criteria provided, single submitter not specified germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.006 Diabetes Mellitus, Insulin-Dependent Three variants were found to be significantly associated with type 1 diabetes (T... BeFree 23922971 Detail
0.293 Diabetes Mellitus, Insulin-Dependent Our results demonstrated that IL2RA rs11594656 and CLEC16A rs725613 are protecti... BeFree 23922971 Detail
0.281 Diabetes Mellitus, Insulin-Dependent Our results demonstrated that IL2RA rs11594656 and CLEC16A rs725613 are protecti... BeFree 23922971 Detail
<0.001 nephritis Our results demonstrated that NLRP1 rs2670660 SNP and the NLRP1 rs12150220-rs267... BeFree 22235789 Detail
<0.001 arthritis Our results demonstrated that NLRP1 rs2670660 SNP and the NLRP1 rs12150220-rs267... BeFree 22235789 Detail
<0.001 Lupus Erythematosus, Systemic Our results demonstrated that NLRP1 rs2670660 SNP and the NLRP1 rs12150220-rs267... BeFree 22235789 Detail
0.363 VITILIGO-ASSOCIATED MULTIPLE AUTOIMMUNE DISEASE SUSCEPTIBILITY 1 (finding) NA CLINVAR Detail
<0.001 Nodular melanoma The NLRP1 variant (rs12150220) was significantly more common in fair-skinned fem... BeFree 22524199 Detail
0.363 VITILIGO-ASSOCIATED MULTIPLE AUTOIMMUNE DISEASE SUSCEPTIBILITY 1 (finding) The PYRIN domain: a novel motif found in apoptosis and inflammation proteins. UNIPROT 11270363 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_033004.4(NLRP1):c.464T>A (p.Leu155His) AND Vitiligo-associated multiple autoimmune disease suscep... ClinVar Detail
NM_033004.4(NLRP1):c.464T>A (p.Leu155His) AND not provided ClinVar Detail
NM_033004.4(NLRP1):c.464T>A (p.Leu155His) AND Corneal intraepithelial dyskeratosis-palmoplantar hype... ClinVar Detail
NM_033004.4(NLRP1):c.464T>A (p.Leu155His) AND Autoinflammation with arthritis and dyskeratosis ClinVar Detail
NM_033004.4(NLRP1):c.464T>A (p.Leu155His) AND Respiratory papillomatosis, juvenile recurrent, congen... ClinVar Detail
NM_033004.4(NLRP1):c.464T>A (p.Leu155His) AND not specified ClinVar Detail
Three variants were found to be significantly associated with type 1 diabetes (T1D): NLRP1 rs1215022... DisGeNET Detail
Our results demonstrated that IL2RA rs11594656 and CLEC16A rs725613 are protective factors of T1D, w... DisGeNET Detail
Our results demonstrated that IL2RA rs11594656 and CLEC16A rs725613 are protective factors of T1D, w... DisGeNET Detail
Our results demonstrated that NLRP1 rs2670660 SNP and the NLRP1 rs12150220-rs2670660 A-G haplotype w... DisGeNET Detail
Our results demonstrated that NLRP1 rs2670660 SNP and the NLRP1 rs12150220-rs2670660 A-G haplotype w... DisGeNET Detail
Our results demonstrated that NLRP1 rs2670660 SNP and the NLRP1 rs12150220-rs2670660 A-G haplotype w... DisGeNET Detail
NA DisGeNET Detail
The NLRP1 variant (rs12150220) was significantly more common in fair-skinned female patients (OR, 1.... DisGeNET Detail
The PYRIN domain: a novel motif found in apoptosis and inflammation proteins. 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
rs12150220 dbSNP
Genome
hg19
Position
chr17:5,485,367-5,485,367
Variant Type
snv
Reference Allele
A
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1192
Mean of sample read depth (HGVD)
37.28
Standard deviation of sample read depth (HGVD)
15.11
Number of reference allele (HGVD)
2284
Number of alternative allele (HGVD)
100
Allele Frequency (HGVD)
0.04194630872483222
Gene Symbol (HGVD)
NLRP1
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))
rs12150220
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0393
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
659
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
7562
East Asian Allele Counts (ExAC)
265
East Asian Heterozygous Counts (ExAC)
253
East Asian Homozygous Counts (ExAC)
6
East Asian Allele Frequency (ExAC)
0.035043639248875956
Chromosome Counts in All Race (ExAC)
113710
Allele Counts in All Race (ExAC)
42635
Heterozygous Counts in All Race (ExAC)
24653
Homozygous Counts in All Race (ExAC)
8991
Allele Frequency in All Race (ExAC)
0.3749450356169202
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