chr3:37053568:A>G Detail (hg19) (MLH1)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr3:37,053,568-37,053,568 |
| hg38 | chr3:37,012,077-37,012,077 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_001258274.1:c.-69A>G | |
| NM_001167619.1:c.-69A>G | ||
| NM_001258271.1:c.655A>G | NP_001245200.1:p.Ile219Val |
Summary
MGeND
| Clinical significance |
Benign
not provided
|
| Variant entry | 558 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.056 |
| ToMMo:0.050 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.022 |
Prediction
ClinVar
| Clinical Significance |
Benign
|
| Review star |  |
| Show details | |
Disease area statistics
MGeND
| Clinical significance | Last evaluated | Condition | Origin | Submission ID | Submitter | Institute | Citation | Comment | Image |
|---|---|---|---|---|---|---|---|---|---|
|
not provided
|
colorectal cancer |
germline
|
MGS000060
(TMGS000107) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
Ovarian cancer |
germline
|
MGS000060
(TMGS000107) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
Bladder cancer |
germline
|
MGS000060
(TMGS000107) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
Cervical cancer |
germline
|
MGS000060
(TMGS000107) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
renal pelvis cancer |
germline
|
MGS000060
(TMGS000107) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
small intestinal cancer |
germline
|
MGS000060
(TMGS000107) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
cancer |
germline
|
MGS000060
(TMGS000107) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
Breast cancer |
germline
|
MGS000060
(TMGS000107) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
gastric cancer |
germline
|
MGS000060
(TMGS000107) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
Endometrial cancer |
germline
|
MGS000060
(TMGS000107) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
Benign
|
Centenarian |
germline
|
MGS000068
(TMGS000140) |
Kenjiro Kosaki | Keio University | ||||
|
Benign
|
2020/04/20 | upper third of oesophagus |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | middle third of oesophagus |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | lower third of oesophagus |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | oesophagus, unspecified |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | fundus of stomach |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | body of stomach |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | pyloric antrum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | stomach, unspecified |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | jejunum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | small intestine, unspecified |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | caecum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | ascending colon |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | transverse colon |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | descending colon |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | sigmoid colon |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | colon, unspecified |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | malignant neoplasm of rectosigmoid junction |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | malignant neoplasm of rectum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | liver cell carcinoma |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | intrahepatic bile duct carcinoma |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | malignant neoplasm of gallbladder |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | extrahepatic bile duct |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | ampulla of vater |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | head of pancreas |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | body of pancreas |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | tail of pancreas |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | ill-defined sites within the digestive system |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | bronchus or lung, unspecified |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan |
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Benign
|
2013-09-05 | reviewed by expert panel | Lynch syndrome |
germline
|
Detail |
|
Benign
|
2023-11-30 | criteria provided, multiple submitters, no conflicts | not provided |
germline
|
Detail |
|
Benign
|
2014-06-24 | criteria provided, multiple submitters, no conflicts | not specified |
germline
unknown
|
Detail |
|
Benign
|
2020-01-10 | criteria provided, multiple submitters, no conflicts | Hereditary cancer-predisposing syndrome |
germline
|
Detail |
|
Benign
|
2017-08-18 | criteria provided, single submitter | Lynch syndrome 1 |
germline
|
Detail |
|
Benign
|
2023-07-07 | criteria provided, multiple submitters, no conflicts | Colorectal cancer, hereditary nonpolyposis, type 2 |
germline
|
Detail |
|
Benign
|
2024-02-01 | criteria provided, single submitter | Hereditary nonpolyposis colorectal neoplasms |
germline
|
Detail |
|
Benign
|
no assertion criteria provided |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.085 | Malignant neoplasm of breast | Using data/samples collected from the first 752 Caucasians and 141 African-Ameri... | BeFree | 18701435 | Detail |
| 0.008 | breast carcinoma | Using data/samples collected from the first 752 Caucasians and 141 African-Ameri... | BeFree | 18701435 | Detail |
| 0.015 | Malignant neoplasm of breast | Using data/samples collected from the first 752 Caucasians and 141 African-Ameri... | BeFree | 18701435 | Detail |
| 0.011 | breast carcinoma | Using data/samples collected from the first 752 Caucasians and 141 African-Ameri... | BeFree | 18701435 | Detail |
| 0.002 | adenoma | In a Minnesota-based case-control study of individuals with adenomas (N=401), hy... | BeFree | 16771955 | Detail |
| 0.002 | breast carcinoma | Using data/samples collected from the first 752 Caucasians and 141 African-Ameri... | BeFree | 18701435 | Detail |
| 0.009 | Malignant neoplasm of breast | Using data/samples collected from the first 752 Caucasians and 141 African-Ameri... | BeFree | 18701435 | Detail |
| 0.019 | Malignant neoplasm of breast | Using data/samples collected from the first 752 Caucasians and 141 African-Ameri... | BeFree | 18701435 | Detail |
| 0.001 | breast carcinoma | Using data/samples collected from the first 752 Caucasians and 141 African-Ameri... | BeFree | 18701435 | Detail |
| 0.004 | breast carcinoma | Using data/samples collected from the first 752 Caucasians and 141 African-Ameri... | BeFree | 18701435 | Detail |
| <0.001 | polyps | In a Minnesota-based case-control study of individuals with adenomas (N=401), hy... | BeFree | 16771955 | Detail |
| 0.018 | breast carcinoma | Using data/samples collected from the first 752 Caucasians and 141 African-Ameri... | BeFree | 18701435 | Detail |
| <0.001 | Hyperplastic Polyp | In a Minnesota-based case-control study of individuals with adenomas (N=401), hy... | BeFree | 16771955 | Detail |
| 0.023 | Malignant neoplasm of breast | Using data/samples collected from the first 752 Caucasians and 141 African-Ameri... | BeFree | 18701435 | Detail |
| 0.013 | Malignant neoplasm of breast | Using data/samples collected from the first 752 Caucasians and 141 African-Ameri... | BeFree | 18701435 | Detail |
| 0.002 | breast carcinoma | Using data/samples collected from the first 752 Caucasians and 141 African-Ameri... | BeFree | 18701435 | Detail |
| 0.013 | polyps | In a Minnesota-based case-control study of individuals with adenomas (N=401), hy... | BeFree | 16771955 | Detail |
| 0.098 | Malignant neoplasm of breast | Using data/samples collected from the first 752 Caucasians and 141 African-Ameri... | BeFree | 18701435 | Detail |
| <0.001 | Polyp of large intestine | In a Minnesota-based case-control study of individuals with adenomas (N=401), hy... | BeFree | 16771955 | Detail |
| 0.015 | Malignant neoplasm of ovary | When the analyses were restricted to serous type ovarian cancer, two SNPs showed... | BeFree | 18723338 | Detail |
| <0.001 | Hereditary pancreatitis | Second, the samples from Finnish hereditary prostate cancer (HPC) families were ... | BeFree | 16963262 | Detail |
| 0.329 | Hereditary Nonpolyposis Colorectal Cancer | Evaluation of MLH1 I219V polymorphism in unrelated South American individuals su... | BeFree | 23060557 | Detail |
| 0.329 | Hereditary Nonpolyposis Colorectal Cancer | The approach was validated by transfecting cDNA of wild-type (WT) MLH1, cDNAs be... | BeFree | 16982745 | Detail |
| 0.012 | ulcerative colitis | Evaluation of the MLH1 I219V alteration in DNA mismatch repair activity and ulce... | BeFree | 18200512 | Detail |
| 0.020 | colon carcinoma | Statistically significant interactions were observed between: MLH1 -93G>A and... | BeFree | 18523027 | Detail |
| 0.332 | Hereditary Nonpolyposis Colorectal Cancer | To evaluate the mutL homolog 1 (MLH1) I219V polymorphism in 124 unrelated South ... | BeFree | 23060557 | Detail |
| 0.003 | Malignant neoplasm of ovary | When the analyses were restricted to serous type ovarian cancer, two SNPs showed... | BeFree | 18723338 | Detail |
| 0.002 | ovarian carcinoma | When the analyses were restricted to serous type ovarian cancer, two SNPs showed... | BeFree | 18723338 | Detail |
| 0.010 | ovarian carcinoma | When the analyses were restricted to serous type ovarian cancer, two SNPs showed... | BeFree | 18723338 | Detail |
| 0.012 | ulcerative colitis | I219V polymorphism in hMLH1 gene in patients affected with ulcerative colitis. | BeFree | 19371218 | Detail |
| 0.005 | breast carcinoma | We observed two two-way SNP-SNP interactions (APEX1-rs1130409 and RPAP1-rs229738... | BeFree | 23755158 | Detail |
| 0.059 | Malignant neoplasm of breast | We observed two two-way SNP-SNP interactions (APEX1-rs1130409 and RPAP1-rs229738... | BeFree | 23755158 | Detail |
| <0.001 | breast carcinoma | We observed two two-way SNP-SNP interactions (APEX1-rs1130409 and RPAP1-rs229738... | BeFree | 23755158 | Detail |
| 0.022 | Malignant neoplasm of breast | We observed two two-way SNP-SNP interactions (APEX1-rs1130409 and RPAP1-rs229738... | BeFree | 23755158 | Detail |
| <0.001 | Malignant neoplasm of breast | We observed two two-way SNP-SNP interactions (APEX1-rs1130409 and RPAP1-rs229738... | BeFree | 23755158 | Detail |
| 0.008 | breast carcinoma | We observed two two-way SNP-SNP interactions (APEX1-rs1130409 and RPAP1-rs229738... | BeFree | 23755158 | Detail |
| 0.021 | breast carcinoma | We observed two two-way SNP-SNP interactions (APEX1-rs1130409 and RPAP1-rs229738... | BeFree | 23755158 | Detail |
| 0.019 | Malignant neoplasm of breast | We observed two two-way SNP-SNP interactions (APEX1-rs1130409 and RPAP1-rs229738... | BeFree | 23755158 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_000249.4(MLH1):c.655A>G (p.Ile219Val) AND Lynch syndrome | ClinVar | Detail |
| NM_000249.4(MLH1):c.655A>G (p.Ile219Val) AND not provided | ClinVar | Detail |
| NM_000249.4(MLH1):c.655A>G (p.Ile219Val) AND not specified | ClinVar | Detail |
| NM_000249.4(MLH1):c.655A>G (p.Ile219Val) AND Hereditary cancer-predisposing syndrome | ClinVar | Detail |
| NM_000249.4(MLH1):c.655A>G (p.Ile219Val) AND Lynch syndrome 1 | ClinVar | Detail |
| NM_000249.4(MLH1):c.655A>G (p.Ile219Val) AND Colorectal cancer, hereditary nonpolyposis, type 2 | ClinVar | Detail |
| NM_000249.4(MLH1):c.655A>G (p.Ile219Val) AND Hereditary nonpolyposis colorectal neoplasms | ClinVar | Detail |
| NM_000249.4(MLH1):c.655A>G (p.Ile219Val) AND Malignant tumor of breast | ClinVar | Detail |
| Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... | DisGeNET | Detail |
| Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... | DisGeNET | Detail |
| Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... | DisGeNET | Detail |
| Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... | DisGeNET | Detail |
| In a Minnesota-based case-control study of individuals with adenomas (N=401), hyperplastic polyps (N... | DisGeNET | Detail |
| Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... | DisGeNET | Detail |
| Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... | DisGeNET | Detail |
| Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... | DisGeNET | Detail |
| Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... | DisGeNET | Detail |
| Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... | DisGeNET | Detail |
| In a Minnesota-based case-control study of individuals with adenomas (N=401), hyperplastic polyps (N... | DisGeNET | Detail |
| Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... | DisGeNET | Detail |
| In a Minnesota-based case-control study of individuals with adenomas (N=401), hyperplastic polyps (N... | DisGeNET | Detail |
| Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... | DisGeNET | Detail |
| Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... | DisGeNET | Detail |
| Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... | DisGeNET | Detail |
| In a Minnesota-based case-control study of individuals with adenomas (N=401), hyperplastic polyps (N... | DisGeNET | Detail |
| Using data/samples collected from the first 752 Caucasians and 141 African-Americans in an ongoing c... | DisGeNET | Detail |
| In a Minnesota-based case-control study of individuals with adenomas (N=401), hyperplastic polyps (N... | DisGeNET | Detail |
| When the analyses were restricted to serous type ovarian cancer, two SNPs showed marginal significan... | DisGeNET | Detail |
| Second, the samples from Finnish hereditary prostate cancer (HPC) families were used for the screeni... | DisGeNET | Detail |
| Evaluation of MLH1 I219V polymorphism in unrelated South American individuals suspected of having Ly... | DisGeNET | Detail |
| The approach was validated by transfecting cDNA of wild-type (WT) MLH1, cDNAs bearing two previously... | DisGeNET | Detail |
| Evaluation of the MLH1 I219V alteration in DNA mismatch repair activity and ulcerative colitis. | DisGeNET | Detail |
| Statistically significant interactions were observed between: MLH1 -93G>A and smoking (MSI-negati... | DisGeNET | Detail |
| To evaluate the mutL homolog 1 (MLH1) I219V polymorphism in 124 unrelated South American individuals... | DisGeNET | Detail |
| When the analyses were restricted to serous type ovarian cancer, two SNPs showed marginal significan... | DisGeNET | Detail |
| When the analyses were restricted to serous type ovarian cancer, two SNPs showed marginal significan... | DisGeNET | Detail |
| When the analyses were restricted to serous type ovarian cancer, two SNPs showed marginal significan... | DisGeNET | Detail |
| I219V polymorphism in hMLH1 gene in patients affected with ulcerative colitis. | DisGeNET | Detail |
| We observed two two-way SNP-SNP interactions (APEX1-rs1130409 and RPAP1-rs2297381; MLH1-rs1799977 an... | DisGeNET | Detail |
| We observed two two-way SNP-SNP interactions (APEX1-rs1130409 and RPAP1-rs2297381; MLH1-rs1799977 an... | DisGeNET | Detail |
| We observed two two-way SNP-SNP interactions (APEX1-rs1130409 and RPAP1-rs2297381; MLH1-rs1799977 an... | DisGeNET | Detail |
| We observed two two-way SNP-SNP interactions (APEX1-rs1130409 and RPAP1-rs2297381; MLH1-rs1799977 an... | DisGeNET | Detail |
| We observed two two-way SNP-SNP interactions (APEX1-rs1130409 and RPAP1-rs2297381; MLH1-rs1799977 an... | DisGeNET | Detail |
| We observed two two-way SNP-SNP interactions (APEX1-rs1130409 and RPAP1-rs2297381; MLH1-rs1799977 an... | DisGeNET | Detail |
| We observed two two-way SNP-SNP interactions (APEX1-rs1130409 and RPAP1-rs2297381; MLH1-rs1799977 an... | DisGeNET | Detail |
| We observed two two-way SNP-SNP interactions (APEX1-rs1130409 and RPAP1-rs2297381; MLH1-rs1799977 an... | 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
- rs1799977 dbSNP
- Genome
- hg19
- Position
- chr3:37,053,568-37,053,568
- Variant Type
- snv
- Reference Allele
- A
- Alternative Allele
- G
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1191
- Mean of sample read depth (HGVD)
- 36.30
- Standard deviation of sample read depth (HGVD)
- 21.08
- Number of reference allele (HGVD)
- 2248
- Number of alternative allele (HGVD)
- 134
- Allele Frequency (HGVD)
- 0.056255247691015954
- Gene Symbol (HGVD)
- MLH1
- 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))
- rs1799977
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0504
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 845
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8650
- East Asian Allele Counts (ExAC)
- 191
- East Asian Heterozygous Counts (ExAC)
- 187
- East Asian Homozygous Counts (ExAC)
- 2
- East Asian Allele Frequency (ExAC)
- 0.02208092485549133
- Chromosome Counts in All Race (ExAC)
- 121236
- Allele Counts in All Race (ExAC)
- 28192
- Heterozygous Counts in All Race (ExAC)
- 20186
- Homozygous Counts in All Race (ExAC)
- 4003
- Allele Frequency in All Race (ExAC)
- 0.2325381899765746
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