chr2:234183368:A>G Detail (hg19) (ATG16L1)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr2:234,183,368-234,183,368 |
| hg38 | chr2:233,274,722-233,274,722 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_198890.2:c.409A>G | NP_942593.2:p.Thr137Ala |
| NM_001190266.1:c.898A>G | NP_001177195.1:p.Thr300Ala | |
| NM_001190267.1:c.898A>G | NP_001177196.1:p.Thr300Ala |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.246 |
| ToMMo:0.220 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.333 |
Prediction
ClinVar
| Clinical Significance |
Benign
|
| Review star |  |
| Show details | |
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
risk factor
|
2014-02-27 | no assertion criteria provided | Inflammatory bowel disease 10, susceptibility to |
germline
|
Detail |
|
Benign
|
2015-02-24 | criteria provided, single submitter | not specified |
germline
|
Detail |
|
Benign
|
2019-10-17 | criteria provided, single submitter | ATG16L1-related disorder |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| <0.001 | obesity | Prior to multiple testing correction, univariate analysis associated APOE rs4293... | BeFree | 26043189 | Detail |
| 0.008 | obesity | Prior to multiple testing correction, univariate analysis associated APOE rs4293... | BeFree | 26043189 | Detail |
| 0.196 | obesity | Prior to multiple testing correction, univariate analysis associated APOE rs4293... | BeFree | 26043189 | Detail |
| 0.368 | Crohn Disease | Detection of Mycobacterium avium subspecies paratuberculosis in patients with Cr... | BeFree | 24522266 | Detail |
| 0.145 | Crohn Disease | Detection of Mycobacterium avium subspecies paratuberculosis in patients with Cr... | BeFree | 24522266 | Detail |
| 0.368 | Crohn Disease | To investigate the interaction of interleukin-23 receptor (IL23R) (rs1004819 and... | BeFree | 20066736 | Detail |
| 0.371 | Crohn Disease | To investigate the interaction of interleukin-23 receptor (IL23R) (rs1004819 and... | BeFree | 20066736 | Detail |
| 0.560 | Crohn Disease | To investigate the interaction of interleukin-23 receptor (IL23R) (rs1004819 and... | BeFree | 20066736 | Detail |
| 0.050 | Crohn Disease | To investigate the interaction of interleukin-23 receptor (IL23R) (rs1004819 and... | BeFree | 20066736 | Detail |
| 0.170 | Crohn Disease | The aim of this study was to determine the role of the ATG16L1 (rs2241880) and I... | BeFree | 19491842 | Detail |
| 0.368 | Crohn Disease | The aim of this study was to determine the role of the ATG16L1 (rs2241880) and I... | BeFree | 19491842 | Detail |
| 0.124 | ulcerative colitis | In conclusion, our results confirm the ATG16L1 rs2241880 and IRGM rs13361189 and... | BeFree | 19491842 | Detail |
| 0.033 | ulcerative colitis | In conclusion, our results confirm the ATG16L1 rs2241880 and IRGM rs13361189 and... | BeFree | 19491842 | Detail |
| 0.080 | Crohn Disease | We confirmed a strong association between three NOD2/CARD15 gene variants (Pro26... | BeFree | 18715515 | Detail |
| 0.560 | Crohn Disease | We confirmed a strong association between three NOD2/CARD15 gene variants (Pro26... | BeFree | 18715515 | Detail |
| 0.080 | Crohn Disease | We confirmed a strong association between three NOD2/CARD15 gene variants (Pro26... | BeFree | 18715515 | Detail |
| 0.368 | Crohn Disease | We confirmed a strong association between three NOD2/CARD15 gene variants (Pro26... | BeFree | 18715515 | Detail |
| 0.368 | Crohn Disease | The ATG16L1 gene variants rs2241879 and rs2241880 (T300A) are strongly associate... | BeFree | 18162085 | Detail |
| 0.033 | ulcerative colitis | In addition, the carriage of T300A variant alleles conferred a protective effect... | BeFree | 25159710 | Detail |
| 0.368 | Crohn Disease | However a possible role of ATG16L1 (T300A) on CD phenotype was suggested. | BeFree | 25159710 | Detail |
| 0.368 | Crohn Disease | A genome-wide scan of Ashkenazi Jewish Crohn's disease suggests novel susceptibi... | GWASCAT | 22412388 | Detail |
| 0.368 | Crohn Disease | Genome-wide association studies have described an association of the ATG16L1 (au... | BeFree | 19659808 | Detail |
| 0.033 | ulcerative colitis | The ATG16L1 T300A polymorphism contributes to susceptibility to CD and UC in adu... | BeFree | 20222171 | Detail |
| 0.397 | Inflammatory Bowel Diseases | Our aims were: to replicate the ATG16L1 Thr300Ala association with inflammatory ... | BeFree | 19575361 | Detail |
| 0.560 | Crohn Disease | We found a statistically significant interaction with respect to Crohn disease r... | BeFree | 17200669 | Detail |
| 0.368 | Crohn Disease | Publications addressing the relationship between rs2241880/T300A polymorphism of... | BeFree | 20222171 | Detail |
| 0.368 | Crohn Disease | Thr300Ala polymorphism in ATG16L1 was reported as a susceptibility factor to Cro... | BeFree | 19575361 | Detail |
| 0.033 | ulcerative colitis | With respect to ATG16L1, the G allele of SNP rs2241880 has been shown in multipl... | BeFree | 18366306 | Detail |
| 0.340 | Inflammatory Bowel Diseases | Our aims were: to replicate the ATG16L1 Thr300Ala association with inflammatory ... | BeFree | 19575361 | Detail |
| 0.173 | Inflammatory Bowel Diseases | T300A polymorphism of ATG16L1 and susceptibility to inflammatory bowel diseases:... | BeFree | 20222171 | Detail |
| 0.120 | Crohn Disease | A genome-wide scan of Ashkenazi Jewish Crohn's disease suggests novel susceptibi... | GWASCAT | 22412388 | Detail |
| 0.120 | Crohn Disease | Genome-wide association study identifies new susceptibility loci for Crohn disea... | GWASCAT | 17435756 | Detail |
| 0.368 | Crohn Disease | ATG16L1 T300A polymorphism and Crohn's disease susceptibility: evidence from 13,... | BeFree | 19337756 | Detail |
| 0.173 | Inflammatory Bowel Diseases | ATG16L1 T300A shows strong associations with disease subgroups in a large Austra... | BeFree | 18671817 | Detail |
| <0.001 | irritable bowel syndrome | ATG16L1 T300A shows strong associations with disease subgroups in a large Austra... | BeFree | 18671817 | Detail |
| 0.173 | Inflammatory Bowel Diseases | Role of ATG16L1 Thr300Ala polymorphism in inflammatory bowel disease: a Study in... | BeFree | 19575361 | Detail |
| 0.368 | Crohn Disease | T300A variant of autophagy ATG16L1 gene is associated with decreased antigen sam... | BeFree | 24022642 | Detail |
| 0.033 | ulcerative colitis | We confirm the strong association between T300A and CD, specifically ileal subph... | BeFree | 18671817 | Detail |
| 0.368 | Crohn Disease | Genome-wide association study identifies new susceptibility loci for Crohn disea... | GWASCAT | 17435756 | Detail |
| 0.173 | Inflammatory Bowel Diseases | IL23R R381Q and ATG16L1 T300A are strongly associated with Crohn's disease in a ... | BeFree | 17894849 | Detail |
| 0.234 | ulcerative colitis | One hundred and eighty unrelated IBD patients [57 Crohn's disease (CD) and 123 u... | BeFree | 20082483 | Detail |
| 0.560 | Crohn Disease | One hundred and eighty unrelated IBD patients [57 Crohn's disease (CD) and 123 u... | BeFree | 20082483 | Detail |
| 0.371 | Crohn Disease | IL23R R381Q and ATG16L1 T300A are strongly associated with Crohn's disease in a ... | BeFree | 17894849 | Detail |
| 0.368 | Crohn Disease | One hundred and eighty unrelated IBD patients [57 Crohn's disease (CD) and 123 u... | BeFree | 20082483 | Detail |
| 0.397 | Inflammatory Bowel Diseases | rs11209026 and rs2241880 genotype distributions were examined both within IBD cl... | BeFree | 17894849 | Detail |
| 0.368 | Crohn Disease | IL23R R381Q and ATG16L1 T300A are strongly associated with Crohn's disease in a ... | BeFree | 17894849 | Detail |
| 0.033 | ulcerative colitis | One hundred and eighty unrelated IBD patients [57 Crohn's disease (CD) and 123 u... | BeFree | 20082483 | Detail |
| 0.371 | Crohn Disease | One hundred and eighty unrelated IBD patients [57 Crohn's disease (CD) and 123 u... | BeFree | 20082483 | Detail |
| 0.340 | Inflammatory Bowel Diseases | IL23R R381Q and ATG16L1 T300A are strongly associated with Crohn's disease in a ... | BeFree | 17894849 | Detail |
| 0.327 | ulcerative colitis | One hundred and eighty unrelated IBD patients [57 Crohn's disease (CD) and 123 u... | BeFree | 20082483 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_030803.7(ATG16L1):c.898A>G (p.Thr300Ala) AND Inflammatory bowel disease 10, susceptibility to | ClinVar | Detail |
| NM_030803.7(ATG16L1):c.898A>G (p.Thr300Ala) AND not specified | ClinVar | Detail |
| NM_030803.7(ATG16L1):c.898A>G (p.Thr300Ala) AND ATG16L1-related disorder | ClinVar | Detail |
| Prior to multiple testing correction, univariate analysis associated APOE rs429358, rs7412 and ATG16... | DisGeNET | Detail |
| Prior to multiple testing correction, univariate analysis associated APOE rs429358, rs7412 and ATG16... | DisGeNET | Detail |
| Prior to multiple testing correction, univariate analysis associated APOE rs429358, rs7412 and ATG16... | DisGeNET | Detail |
| Detection of Mycobacterium avium subspecies paratuberculosis in patients with Crohn's disease is unr... | DisGeNET | Detail |
| Detection of Mycobacterium avium subspecies paratuberculosis in patients with Crohn's disease is unr... | DisGeNET | Detail |
| To investigate the interaction of interleukin-23 receptor (IL23R) (rs1004819 and rs2201841), autopha... | DisGeNET | Detail |
| To investigate the interaction of interleukin-23 receptor (IL23R) (rs1004819 and rs2201841), autopha... | DisGeNET | Detail |
| To investigate the interaction of interleukin-23 receptor (IL23R) (rs1004819 and rs2201841), autopha... | DisGeNET | Detail |
| To investigate the interaction of interleukin-23 receptor (IL23R) (rs1004819 and rs2201841), autopha... | DisGeNET | Detail |
| The aim of this study was to determine the role of the ATG16L1 (rs2241880) and IRGM (rs13361189 and ... | DisGeNET | Detail |
| The aim of this study was to determine the role of the ATG16L1 (rs2241880) and IRGM (rs13361189 and ... | DisGeNET | Detail |
| In conclusion, our results confirm the ATG16L1 rs2241880 and IRGM rs13361189 and rs4958847 polymorph... | DisGeNET | Detail |
| In conclusion, our results confirm the ATG16L1 rs2241880 and IRGM rs13361189 and rs4958847 polymorph... | DisGeNET | Detail |
| We confirmed a strong association between three NOD2/CARD15 gene variants (Pro268Ser, OR = 2.52, 95%... | DisGeNET | Detail |
| We confirmed a strong association between three NOD2/CARD15 gene variants (Pro268Ser, OR = 2.52, 95%... | DisGeNET | Detail |
| We confirmed a strong association between three NOD2/CARD15 gene variants (Pro268Ser, OR = 2.52, 95%... | DisGeNET | Detail |
| We confirmed a strong association between three NOD2/CARD15 gene variants (Pro268Ser, OR = 2.52, 95%... | DisGeNET | Detail |
| The ATG16L1 gene variants rs2241879 and rs2241880 (T300A) are strongly associated with susceptibilit... | DisGeNET | Detail |
| In addition, the carriage of T300A variant alleles conferred a protective effect in UC. | DisGeNET | Detail |
| However a possible role of ATG16L1 (T300A) on CD phenotype was suggested. | DisGeNET | Detail |
| A genome-wide scan of Ashkenazi Jewish Crohn's disease suggests novel susceptibility loci. | DisGeNET | Detail |
| Genome-wide association studies have described an association of the ATG16L1 (autophagy 16-like 1) g... | DisGeNET | Detail |
| The ATG16L1 T300A polymorphism contributes to susceptibility to CD and UC in adults, but different i... | DisGeNET | Detail |
| Our aims were: to replicate the ATG16L1 Thr300Ala association with inflammatory bowel disease (IBD) ... | DisGeNET | Detail |
| We found a statistically significant interaction with respect to Crohn disease risk between rs224188... | DisGeNET | Detail |
| Publications addressing the relationship between rs2241880/T300A polymorphism of ATG16L1 and Crohn's... | DisGeNET | Detail |
| Thr300Ala polymorphism in ATG16L1 was reported as a susceptibility factor to Crohn's disease (CD). | DisGeNET | Detail |
| With respect to ATG16L1, the G allele of SNP rs2241880 has been shown in multiple association studie... | DisGeNET | Detail |
| Our aims were: to replicate the ATG16L1 Thr300Ala association with inflammatory bowel disease (IBD) ... | DisGeNET | Detail |
| T300A polymorphism of ATG16L1 and susceptibility to inflammatory bowel diseases: a meta-analysis. | DisGeNET | Detail |
| A genome-wide scan of Ashkenazi Jewish Crohn's disease suggests novel susceptibility loci. | DisGeNET | Detail |
| Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates au... | DisGeNET | Detail |
| ATG16L1 T300A polymorphism and Crohn's disease susceptibility: evidence from 13,022 cases and 17,532... | DisGeNET | Detail |
| ATG16L1 T300A shows strong associations with disease subgroups in a large Australian IBD population:... | DisGeNET | Detail |
| ATG16L1 T300A shows strong associations with disease subgroups in a large Australian IBD population:... | DisGeNET | Detail |
| Role of ATG16L1 Thr300Ala polymorphism in inflammatory bowel disease: a Study in the Spanish populat... | DisGeNET | Detail |
| T300A variant of autophagy ATG16L1 gene is associated with decreased antigen sampling and processing... | DisGeNET | Detail |
| We confirm the strong association between T300A and CD, specifically ileal subphenotype, and also re... | DisGeNET | Detail |
| Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates au... | DisGeNET | Detail |
| IL23R R381Q and ATG16L1 T300A are strongly associated with Crohn's disease in a study of New Zealand... | DisGeNET | Detail |
| One hundred and eighty unrelated IBD patients [57 Crohn's disease (CD) and 123 ulcerative colitis (U... | DisGeNET | Detail |
| One hundred and eighty unrelated IBD patients [57 Crohn's disease (CD) and 123 ulcerative colitis (U... | DisGeNET | Detail |
| IL23R R381Q and ATG16L1 T300A are strongly associated with Crohn's disease in a study of New Zealand... | DisGeNET | Detail |
| One hundred and eighty unrelated IBD patients [57 Crohn's disease (CD) and 123 ulcerative colitis (U... | DisGeNET | Detail |
| rs11209026 and rs2241880 genotype distributions were examined both within IBD clinical subphenotypes... | DisGeNET | Detail |
| IL23R R381Q and ATG16L1 T300A are strongly associated with Crohn's disease in a study of New Zealand... | DisGeNET | Detail |
| One hundred and eighty unrelated IBD patients [57 Crohn's disease (CD) and 123 ulcerative colitis (U... | DisGeNET | Detail |
| One hundred and eighty unrelated IBD patients [57 Crohn's disease (CD) and 123 ulcerative colitis (U... | DisGeNET | Detail |
| IL23R R381Q and ATG16L1 T300A are strongly associated with Crohn's disease in a study of New Zealand... | DisGeNET | Detail |
| One hundred and eighty unrelated IBD patients [57 Crohn's disease (CD) and 123 ulcerative colitis (U... | 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
- rs2241880 dbSNP
- Genome
- hg19
- Position
- chr2:234,183,368-234,183,368
- Variant Type
- snv
- Reference Allele
- A
- Alternative Allele
- G
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 847
- Mean of sample read depth (HGVD)
- 10.94
- Standard deviation of sample read depth (HGVD)
- 15.77
- Number of reference allele (HGVD)
- 1278
- Number of alternative allele (HGVD)
- 416
- Allele Frequency (HGVD)
- 0.24557260920897284
- Gene Symbol (HGVD)
- ATG16L1
- 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))
- rs2241880
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.22
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 3687
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8628
- East Asian Allele Counts (ExAC)
- 2873
- East Asian Heterozygous Counts (ExAC)
- 1945
- East Asian Homozygous Counts (ExAC)
- 464
- East Asian Allele Frequency (ExAC)
- 0.33298562818729716
- Chromosome Counts in All Race (ExAC)
- 121220
- Allele Counts in All Race (ExAC)
- 55495
- Heterozygous Counts in All Race (ExAC)
- 28325
- Homozygous Counts in All Race (ExAC)
- 13585
- Allele Frequency in All Race (ExAC)
- 0.45780399274047184
Genome browser