chr1:66075952:G>C Detail (hg19) (LEPR)

Information

Genome

Assembly Position
hg19 chr1:66,075,952-66,075,952
hg38 chr1:65,610,269-65,610,269 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_002303.5:c.1968G>C NP_002294.2:p.Lys656Asn
NM_001198689.1:c.1968G>C NP_001185618.1:p.Lys656Asn
NM_001003680.3:c.1968G>C NP_001003680.1:p.Lys656Asn
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.083
ToMMo:0.102
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.055

Prediction

ClinVar

Clinical Significance Benign Likely benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 601007 OMIM
HGNC 6554 HGNC
Ensembl ENSG00000116678 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv1822394 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2001-07-01 no assertion criteria provided LEPTIN RECEPTOR POLYMORPHISM germline Detail
Likely benign 2016-06-14 criteria provided, single submitter Monogenic Non-Syndromic Obesity germline Detail
Benign Likely benign 2021-10-18 criteria provided, multiple submitters, no conflicts Obesity due to leptin receptor gene deficiency germline unknown Detail
Benign 2024-01-31 criteria provided, multiple submitters, no conflicts not provided germline Detail
Benign 2017-12-19 criteria provided, single submitter not specified germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.439 obesity Some polymorphic genes involved in the regulation of leptin-the leptin gene (LEP... BeFree 15972940 Detail
0.124 Overweight Three LEPR polymorphisms (Lys(109)Arg, Gln(223)Arg, and Lys(656)Asn) were typed ... BeFree 11443193 Detail
0.641 obesity Three non-synonymous single nucleotide polymorphisms (Q223R, K109R and K656N) of... BeFree 22028824 Detail
0.641 obesity Some polymorphic genes involved in the regulation of leptin-the leptin gene (LEP... BeFree 15972940 Detail
0.002 obesity Some polymorphic genes involved in the regulation of leptin-the leptin gene (LEP... BeFree 15972940 Detail
0.641 obesity Lys656Asn polymorphism of LEPR gene is associated with obesity parameters, insul... BeFree 22530350 Detail
0.641 obesity Lys656Asn polymorphism of leptin receptor gene is related with leptin changes af... BeFree 23266707 Detail
0.003 Acute coronary syndrome To evaluate the effect of atorvastatin on bone mass and markers of bone remodeli... BeFree 19023160 Detail
0.124 Overweight The at risk for overweight/overweight subjects with the Lys656Lys homozygous wil... BeFree 18654948 Detail
0.237 obesity The aim of our study was to investigate the interaction between the tumor necros... BeFree 20814201 Detail
0.239 Diabetes Mellitus, Non-Insulin-Dependent Influence of Lys656Asn polymorphism of leptin receptor gene on insulin resistanc... BeFree 18632178 Detail
0.641 obesity The aim of our study was to investigate the interaction between the tumor necros... BeFree 20814201 Detail
0.440 obesity Lys656Asn polymorphism of leptin receptor gene is related with leptin changes af... BeFree 23266707 Detail
0.440 obesity Leptin receptor Lys656Asn polymorphism is associated with decreased leptin respo... BeFree 16971225 Detail
0.641 obesity Leptin receptor Lys656Asn polymorphism is associated with decreased leptin respo... BeFree 16971225 Detail
0.001 Non-alcoholic Fatty Liver Disease Lys656Asn polymorphism of LEPR gene is associated with obesity parameters, insul... BeFree 22530350 Detail
0.012 Metabolic syndrome X Lys656Asn polymorphism of leptin receptor gene and metabolic syndrome in obese p... BeFree 21744741 Detail
0.440 obesity The aim of our study was to investigate the interaction between the tumor necros... BeFree 20814201 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_002303.6(LEPR):c.1968G>C (p.Lys656Asn) AND LEPTIN RECEPTOR POLYMORPHISM ClinVar Detail
NM_002303.6(LEPR):c.1968G>C (p.Lys656Asn) AND Monogenic Non-Syndromic Obesity ClinVar Detail
NM_002303.6(LEPR):c.1968G>C (p.Lys656Asn) AND Obesity due to leptin receptor gene deficiency ClinVar Detail
NM_002303.6(LEPR):c.1968G>C (p.Lys656Asn) AND not provided ClinVar Detail
NM_002303.6(LEPR):c.1968G>C (p.Lys656Asn) AND not specified ClinVar Detail
Some polymorphic genes involved in the regulation of leptin-the leptin gene (LEP A19G), the leptin r... DisGeNET Detail
Three LEPR polymorphisms (Lys(109)Arg, Gln(223)Arg, and Lys(656)Asn) were typed on genomic DNA of 35... DisGeNET Detail
Three non-synonymous single nucleotide polymorphisms (Q223R, K109R and K656N) of the leptin receptor... DisGeNET Detail
Some polymorphic genes involved in the regulation of leptin-the leptin gene (LEP A19G), the leptin r... DisGeNET Detail
Some polymorphic genes involved in the regulation of leptin-the leptin gene (LEP A19G), the leptin r... DisGeNET Detail
Lys656Asn polymorphism of LEPR gene is associated with obesity parameters, insulin resistance and gl... DisGeNET Detail
Lys656Asn polymorphism of leptin receptor gene is related with leptin changes after a high monounsat... DisGeNET Detail
To evaluate the effect of atorvastatin on bone mass and markers of bone remodeling in patients with ... DisGeNET Detail
The at risk for overweight/overweight subjects with the Lys656Lys homozygous wild type LEPR gene had... DisGeNET Detail
The aim of our study was to investigate the interaction between the tumor necrosis factor-α (TNF-α) ... DisGeNET Detail
Influence of Lys656Asn polymorphism of leptin receptor gene on insulin resistance in patients with d... DisGeNET Detail
The aim of our study was to investigate the interaction between the tumor necrosis factor-α (TNF-α) ... DisGeNET Detail
Lys656Asn polymorphism of leptin receptor gene is related with leptin changes after a high monounsat... DisGeNET Detail
Leptin receptor Lys656Asn polymorphism is associated with decreased leptin response and weight loss ... DisGeNET Detail
Leptin receptor Lys656Asn polymorphism is associated with decreased leptin response and weight loss ... DisGeNET Detail
Lys656Asn polymorphism of LEPR gene is associated with obesity parameters, insulin resistance and gl... DisGeNET Detail
Lys656Asn polymorphism of leptin receptor gene and metabolic syndrome in obese patients. DisGeNET Detail
The aim of our study was to investigate the interaction between the tumor necrosis factor-α (TNF-α) ... 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
rs1805094 dbSNP
Genome
hg19
Position
chr1:66,075,952-66,075,952
Variant Type
snv
Reference Allele
G
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1145
Mean of sample read depth (HGVD)
34.27
Standard deviation of sample read depth (HGVD)
17.94
Number of reference allele (HGVD)
2101
Number of alternative allele (HGVD)
189
Allele Frequency (HGVD)
0.08253275109170306
Gene Symbol (HGVD)
LEPR
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))
rs1805094
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1017
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1704
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8622
East Asian Allele Counts (ExAC)
474
East Asian Heterozygous Counts (ExAC)
450
East Asian Homozygous Counts (ExAC)
12
East Asian Allele Frequency (ExAC)
0.054975643702157274
Chromosome Counts in All Race (ExAC)
120630
Allele Counts in All Race (ExAC)
19051
Heterozygous Counts in All Race (ExAC)
15899
Homozygous Counts in All Race (ExAC)
1576
Allele Frequency in All Race (ExAC)
0.15792920500704635
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