chr5:95728898:C>G Detail (hg19) (CAST, PCSK1, LOC101929710)

Information

Genome

Assembly Position
hg19 chr5:95,728,898-95,728,898
hg38 chr5:96,393,194-96,393,194 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000439.4:c.2069G>C NP_000430.3:p.Ser690Thr
NM_001177875.1:c.1928G>C NP_001171346.1:p.Ser643Thr
Ensemble ENST00000311106.8:c.2069G>C ENST00000311106.8:p.Ser690Thr
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.216
ToMMo:0.210
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.310

Prediction

ClinVar

Clinical Significance Benign Likely benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 162150 OMIM
HGNC 8743 HGNC
Ensembl ENSG00000175426 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv21980906 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Likely benign 2016-06-14 criteria provided, single submitter Monogenic Non-Syndromic Obesity germline Detail
Benign 2018-01-12 criteria provided, single submitter Obesity due to prohormone convertase I deficiency germline Detail
Benign 2017-12-19 criteria provided, single submitter not specified germline Detail
Benign 2024-02-01 criteria provided, multiple submitters, no conflicts not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.097 Diabetes Mellitus, Non-Insulin-Dependent Single nucleotide polymorphisms (SNPs) in PCSK1, namely, rs6234, rs6235, and rs2... BeFree 24964673 Detail
0.230 obesity Association of the rs6235 variant in the proprotein convertase subtilisin/kexin ... BeFree 24140494 Detail
0.230 obesity The obesity-related polymorphism PCSK1 rs6235 is associated with essential hyper... BeFree 22592666 Detail
0.097 Diabetes Mellitus, Non-Insulin-Dependent [Two loci (LARP6 and SGSM2) have not been previously related to metabolic traits... GAD 21873549 Detail
<0.001 Overweight Our study indicates that the PCSK1 rs6235 SNP may contribute to the risk of over... BeFree 24140494 Detail
0.003 obesity Of five studied variants, only two (SEC16B rs10913469, SH2B1 rs4788102) were nom... BeFree 23121087 Detail
0.021 obesity Of five studied variants, only two (SEC16B rs10913469, SH2B1 rs4788102) were nom... BeFree 23121087 Detail
0.153 obesity Of five studied variants, only two (SEC16B rs10913469, SH2B1 rs4788102) were nom... BeFree 23121087 Detail
0.278 obesity Of five studied variants, only two (SEC16B rs10913469, SH2B1 rs4788102) were nom... BeFree 23121087 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000439.5(PCSK1):c.2069G>C (p.Ser690Thr) AND Monogenic Non-Syndromic Obesity ClinVar Detail
NM_000439.5(PCSK1):c.2069G>C (p.Ser690Thr) AND Obesity due to prohormone convertase I deficiency ClinVar Detail
NM_000439.5(PCSK1):c.2069G>C (p.Ser690Thr) AND not specified ClinVar Detail
NM_000439.5(PCSK1):c.2069G>C (p.Ser690Thr) AND not provided ClinVar Detail
Single nucleotide polymorphisms (SNPs) in PCSK1, namely, rs6234, rs6235, and rs271939 have been link... DisGeNET Detail
Association of the rs6235 variant in the proprotein convertase subtilisin/kexin type 1 (PCSK1) gene ... DisGeNET Detail
The obesity-related polymorphism PCSK1 rs6235 is associated with essential hypertension in the Han C... DisGeNET Detail
[Two loci (LARP6 and SGSM2) have not been previously related to metabolic traits, one (MADD) has bee... DisGeNET Detail
Our study indicates that the PCSK1 rs6235 SNP may contribute to the risk of overweight in men and pr... DisGeNET Detail
Of five studied variants, only two (SEC16B rs10913469, SH2B1 rs4788102) were nominally associated wi... DisGeNET Detail
Of five studied variants, only two (SEC16B rs10913469, SH2B1 rs4788102) were nominally associated wi... DisGeNET Detail
Of five studied variants, only two (SEC16B rs10913469, SH2B1 rs4788102) were nominally associated wi... DisGeNET Detail
Of five studied variants, only two (SEC16B rs10913469, SH2B1 rs4788102) were nominally associated wi... 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
rs6235 dbSNP
Genome
hg19
Position
chr5:95,728,898-95,728,898
Variant Type
snv
Reference Allele
C
Alternative Allele
G
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
163.08
Standard deviation of sample read depth (HGVD)
66.97
Number of reference allele (HGVD)
1898
Number of alternative allele (HGVD)
522
Allele Frequency (HGVD)
0.21570247933884298
Gene Symbol (HGVD)
PCSK1
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))
rs6235
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.21
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
3519
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8640
East Asian Allele Counts (ExAC)
2675
East Asian Heterozygous Counts (ExAC)
1901
East Asian Homozygous Counts (ExAC)
387
East Asian Allele Frequency (ExAC)
0.30960648148148145
Chromosome Counts in All Race (ExAC)
121374
Allele Counts in All Race (ExAC)
32196
Heterozygous Counts in All Race (ExAC)
23326
Homozygous Counts in All Race (ExAC)
4435
Allele Frequency in All Race (ExAC)
0.26526274160858176
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