chr2:181678728:T>C Detail (hg38) (NEUROD1, CERKL)

Information

Genome

Assembly Position
hg19 chr2:182,543,455-182,543,455 View the variant detail on this assembly version.
hg38 chr2:181,678,728-181,678,728

HGVS

Type Transcript Protein
RefSeq
Ensemble ENST00000684145.1:c.-455+1702A>G
Type Transcript Protein
RefSeq NM_002500.4:c.133A>G NP_002491.2:p.Thr45Ala
Ensemble ENST00000295108.4:c.133A>G ENST00000295108.4:p.Thr45Ala
ENST00000683430.1:c.133A>G ENST00000683430.1:p.Thr45Ala
Summary

MGeND

Clinical significance Benign
Variant entry 1
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.923
ToMMo:0.918
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.916

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 608381 OMIM
HGNC 21699 HGNC
Ensembl ENSG00000188452 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv9737705 TogoVar
COSMIC
MONDO
Type Database ID Link
Gene MIM 601724 OMIM
HGNC 7762 HGNC
Ensembl ENSG00000162992 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv9737705 TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Benign Centenarian germline MGS000068
(TMGS000140) 		Kenjiro Kosaki Keio University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2019-05-28 criteria provided, single submitter Maturity onset diabetes mellitus in young unknown Detail
Benign 2024-02-01 criteria provided, single submitter not provided germline Detail
Benign 2021-09-05 criteria provided, single submitter maturity-onset diabetes of the young type 6 germline Detail
Benign 2023-10-01 criteria provided, single submitter Retinal dystrophy germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.016 Diabetes Mellitus, Non-Insulin-Dependent Polymorphisms of these genes (Ala45Thr [NEUROD1], Ser199Phe [NEUROG3], and Ala98... BeFree 15277395 Detail
0.283 Diabetes Mellitus, Non-Insulin-Dependent Polymorphisms of these genes (Ala45Thr [NEUROD1], Ser199Phe [NEUROG3], and Ala98... BeFree 15277395 Detail
0.329 Diabetes Mellitus, Non-Insulin-Dependent Polymorphisms of these genes (Ala45Thr [NEUROD1], Ser199Phe [NEUROG3], and Ala98... BeFree 15277395 Detail
0.283 Diabetes Mellitus, Non-Insulin-Dependent NeuroD1 A45T and PAX4 R121W polymorphisms are associated with plasma glucose lev... BeFree 22296034 Detail
0.034 Diabetes Mellitus, Insulin-Dependent Absence of replication in the French population of the association between beta ... BeFree 10633878 Detail
0.034 Diabetes Mellitus, Insulin-Dependent The Ala45Thr polymorphism of BETA2/NeuroD1 gene and susceptibility to type 1 dia... BeFree 12951629 Detail
0.034 Diabetes Mellitus, Insulin-Dependent Lack of association of the Ala(45)Thr polymorphism and other common variants of ... BeFree 15047635 Detail
0.283 Diabetes Mellitus, Non-Insulin-Dependent Evaluation of variant A45T in NEUROD1/BETA2 for its association with type 2 diab... BeFree 23203005 Detail
0.011 Diabetes Mellitus, Insulin-Dependent On the other hand we confirmed that the Ala45Thr variant in NeuroD1/BETA2 may re... BeFree 14694850 Detail
0.034 Diabetes Mellitus, Insulin-Dependent Lack of association of the Ala45Thr variant in the BETA2/NEUROD1 with type 1 dia... BeFree 10808064 Detail
0.283 Diabetes Mellitus, Non-Insulin-Dependent Because the variant of the NeuroD/BETA2 gene (Ala45Thr) is associated with type ... BeFree 10334323 Detail
0.283 Diabetes Mellitus, Non-Insulin-Dependent To evaluate the role of the Ala45Thr variant of BETA2/NEUROD1 in the development... BeFree 10808064 Detail
0.034 Diabetes Mellitus, Insulin-Dependent On the other hand we confirmed that the Ala45Thr variant in NeuroD1/BETA2 may re... BeFree 14694850 Detail
0.003 Diabetes Ala45Thr polymorphism of the NEUROD1 gene and diabetes susceptibility: a meta-an... BeFree 15592940 Detail
0.283 Diabetes Mellitus, Non-Insulin-Dependent The Ala45Thr polymorphism of BETA2/NeuroD1 gene and susceptibility to type 2 dia... BeFree 12861411 Detail
0.034 Diabetes Mellitus, Insulin-Dependent The Ala45Thr polymorphism of NEUROD1 is associated with type 1 diabetes in Brazi... BeFree 16357810 Detail
0.034 Diabetes Mellitus, Insulin-Dependent A meta-analysis assessed whether the Ala45Thr polymorphism of the neurogenic dif... BeFree 15592940 Detail
0.458 Diabetes Mellitus, Non-Insulin-Dependent NeuroD1 A45T and PAX4 R121W polymorphisms are associated with plasma glucose lev... BeFree 22296034 Detail
0.283 Diabetes Mellitus, Non-Insulin-Dependent Ala45Thr variation in neuroD1 gene is associated with early-onset type 2 diabete... BeFree 16773428 Detail
0.034 Diabetes Mellitus, Insulin-Dependent NEUROD polymorphism Ala45Thr is associated with Type 1 diabetes mellitus in Czec... BeFree 12639765 Detail
0.034 Diabetes Mellitus, Insulin-Dependent Because the variant of the NeuroD/BETA2 gene (Ala45Thr) is associated with type ... BeFree 10334323 Detail
0.008 diabetes mellitus Ala45Thr polymorphism of the NEUROD1 gene and diabetes susceptibility: a meta-an... BeFree 15592940 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_002500.5(NEUROD1):c.133A>G (p.Thr45Ala) AND Maturity onset diabetes mellitus in young ClinVar Detail
NM_002500.5(NEUROD1):c.133A>G (p.Thr45Ala) AND not provided ClinVar Detail
NM_002500.5(NEUROD1):c.133A>G (p.Thr45Ala) AND Maturity-onset diabetes of the young type 6 ClinVar Detail
NM_002500.5(NEUROD1):c.133A>G (p.Thr45Ala) AND Retinal dystrophy ClinVar Detail
Polymorphisms of these genes (Ala45Thr [NEUROD1], Ser199Phe [NEUROG3], and Ala98Val [TCF1]) have bee... DisGeNET Detail
Polymorphisms of these genes (Ala45Thr [NEUROD1], Ser199Phe [NEUROG3], and Ala98Val [TCF1]) have bee... DisGeNET Detail
Polymorphisms of these genes (Ala45Thr [NEUROD1], Ser199Phe [NEUROG3], and Ala98Val [TCF1]) have bee... DisGeNET Detail
NeuroD1 A45T and PAX4 R121W polymorphisms are associated with plasma glucose level of repaglinide mo... DisGeNET Detail
Absence of replication in the French population of the association between beta 2/NEUROD-A45T polymo... DisGeNET Detail
The Ala45Thr polymorphism of BETA2/NeuroD1 gene and susceptibility to type 1 diabetes mellitus in ca... DisGeNET Detail
Lack of association of the Ala(45)Thr polymorphism and other common variants of the NeuroD gene with... DisGeNET Detail
Evaluation of variant A45T in NEUROD1/BETA2 for its association with type 2 diabetes mellitus. DisGeNET Detail
On the other hand we confirmed that the Ala45Thr variant in NeuroD1/BETA2 may represent a susceptibi... DisGeNET Detail
Lack of association of the Ala45Thr variant in the BETA2/NEUROD1 with type 1 diabetes in Japanese. DisGeNET Detail
Because the variant of the NeuroD/BETA2 gene (Ala45Thr) is associated with type 1 but not type 2 dia... DisGeNET Detail
To evaluate the role of the Ala45Thr variant of BETA2/NEUROD1 in the development of type 1 or type 2... DisGeNET Detail
On the other hand we confirmed that the Ala45Thr variant in NeuroD1/BETA2 may represent a susceptibi... DisGeNET Detail
Ala45Thr polymorphism of the NEUROD1 gene and diabetes susceptibility: a meta-analysis. DisGeNET Detail
The Ala45Thr polymorphism of BETA2/NeuroD1 gene and susceptibility to type 2 diabetes mellitus in a ... DisGeNET Detail
The Ala45Thr polymorphism of NEUROD1 is associated with type 1 diabetes in Brazilian women. DisGeNET Detail
A meta-analysis assessed whether the Ala45Thr polymorphism of the neurogenic differentiation 1 (NEUR... DisGeNET Detail
NeuroD1 A45T and PAX4 R121W polymorphisms are associated with plasma glucose level of repaglinide mo... DisGeNET Detail
Ala45Thr variation in neuroD1 gene is associated with early-onset type 2 diabetes with or without di... DisGeNET Detail
NEUROD polymorphism Ala45Thr is associated with Type 1 diabetes mellitus in Czech children. DisGeNET Detail
Because the variant of the NeuroD/BETA2 gene (Ala45Thr) is associated with type 1 but not type 2 dia... DisGeNET Detail
Ala45Thr polymorphism of the NEUROD1 gene and diabetes susceptibility: a meta-analysis. 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
rs1801262 dbSNP
Genome
hg38
Position
chr2:181,678,728-181,678,728
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1209
Mean of sample read depth (HGVD)
125.67
Standard deviation of sample read depth (HGVD)
57.57
Number of reference allele (HGVD)
186
Number of alternative allele (HGVD)
2227
Allele Frequency (HGVD)
0.9229175300455864
Gene Symbol (HGVD)
NEUROD1
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))
rs1801262
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.9178
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
15382
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8174
East Asian Allele Counts (ExAC)
7491
East Asian Heterozygous Counts (ExAC)
625
East Asian Homozygous Counts (ExAC)
3433
East Asian Allele Frequency (ExAC)
0.9164423782725716
Chromosome Counts in All Race (ExAC)
116760
Allele Counts in All Race (ExAC)
82053
Heterozygous Counts in All Race (ExAC)
23717
Homozygous Counts in All Race (ExAC)
29168
Allele Frequency in All Race (ExAC)
0.7027492291880781
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