chr5:136055770:C>A Detail (hg38) (TGFBI)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr5:135,391,459-135,391,459 View the variant detail on this assembly version. |
| hg38 | chr5:136,055,770-136,055,770 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_000358.2:c.1501C>A | NP_000349.1:p.Pro501Thr |
| Ensemble | ENST00000442011.7:c.1501C>A | ENST00000442011.7:p.Pro501Thr |
Summary
MGeND
| Clinical significance |
Benign
Pathogenic
|
| Variant entry | 2 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.009 |
| ToMMo:0.014 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.004 |
Prediction
ClinVar
| Clinical Significance | Conflicting classifications of pathogenicity |
| Review star |  |
| Show details | |
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 | ||||
|
Pathogenic
|
other |
germline
|
MGS000082
(TMGS000165) |
Kenjiro Kosaki Kenjiro Kosaki |
Keio University Mutation View |
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Pathogenic
|
2002-11-15 | no assertion criteria provided | Corneal dystrophy, lattice type 3A |
germline
|
Detail |
Likely pathogenic
|
2017-04-28 | criteria provided, single submitter | corneal dystrophy |
germline
|
Detail |
|
Likely pathogenic
|
2021-09-30 | criteria provided, single submitter | not provided |
germline
|
Detail |
Uncertain significance
|
2022-05-04 | criteria provided, single submitter | not specified |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.361 | Corneal Dystrophy, Lattice Type IIIA | In our study, thirty patients from five pedigrees and ten sporadic patients were... | BeFree | 21462384 | Detail |
| 0.002 | Corneal dystrophy, Lattice type 3 | Q118X mutation of M1S1 gene caused gelatinous drop-like corneal dystrophy: the P... | BeFree | 11004271 | Detail |
| 0.361 | Corneal Dystrophy, Lattice Type IIIA | Amyloid and Pro501 Thr-mutated (beta)ig-h3 gene product colocalize in lattice co... | BeFree | 10218700 | Detail |
| 0.365 | Corneal dystrophy, Lattice type 3 | Q118X mutation of M1S1 gene caused gelatinous drop-like corneal dystrophy: the P... | BeFree | 11004271 | Detail |
| 0.008 | Familial Amyloid Polyneuropathy, Type V | Although the P501T of the BIGH3 gene found in this pedigree was precisely the on... | BeFree | 11004271 | Detail |
| 0.361 | Corneal Dystrophy, Lattice Type IIIA | Association of autosomal dominantly inherited corneal dystrophies with BIGH3 gen... | UNIPROT | 11024425 | Detail |
| 0.361 | Corneal Dystrophy, Lattice Type IIIA | NA | CLINVAR | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_000358.3(TGFBI):c.1501C>A (p.Pro501Thr) AND Corneal dystrophy, lattice type 3A | ClinVar | Detail |
| NM_000358.3(TGFBI):c.1501C>A (p.Pro501Thr) AND Corneal dystrophy | ClinVar | Detail |
| NM_000358.3(TGFBI):c.1501C>A (p.Pro501Thr) AND not provided | ClinVar | Detail |
| NM_000358.3(TGFBI):c.1501C>A (p.Pro501Thr) AND not specified | ClinVar | Detail |
| In our study, thirty patients from five pedigrees and ten sporadic patients were diagnosed as four T... | DisGeNET | Detail |
| Q118X mutation of M1S1 gene caused gelatinous drop-like corneal dystrophy: the P501T of BIGH3 gene f... | DisGeNET | Detail |
| Amyloid and Pro501 Thr-mutated (beta)ig-h3 gene product colocalize in lattice corneal dystrophy type... | DisGeNET | Detail |
| Q118X mutation of M1S1 gene caused gelatinous drop-like corneal dystrophy: the P501T of BIGH3 gene f... | DisGeNET | Detail |
| Although the P501T of the BIGH3 gene found in this pedigree was precisely the one reported for latti... | DisGeNET | Detail |
| Association of autosomal dominantly inherited corneal dystrophies with BIGH3 gene mutations in Japan... | DisGeNET | Detail |
| NA | 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
- rs121909212 dbSNP
- Genome
- hg38
- Position
- chr5:136,055,770-136,055,770
- Variant Type
- snv
- Reference Allele
- C
- Alternative Allele
- A
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1197
- Mean of sample read depth (HGVD)
- 51.50
- Standard deviation of sample read depth (HGVD)
- 26.20
- Number of reference allele (HGVD)
- 2373
- Number of alternative allele (HGVD)
- 21
- Allele Frequency (HGVD)
- 0.008771929824561403
- Gene Symbol (HGVD)
- TGFBI
- 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))
- rs121909212
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0144
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 241
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8168
- East Asian Allele Counts (ExAC)
- 33
- East Asian Heterozygous Counts (ExAC)
- 33
- East Asian Homozygous Counts (ExAC)
- 0
- East Asian Allele Frequency (ExAC)
- 0.004040156709108717
- Chromosome Counts in All Race (ExAC)
- 113076
- Allele Counts in All Race (ExAC)
- 36
- Heterozygous Counts in All Race (ExAC)
- 36
- Homozygous Counts in All Race (ExAC)
- 0
- Allele Frequency in All Race (ExAC)
- 3.183699458771092E-4
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