chr12:101753409:G>A Detail (hg38) (GNPTAB)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr12:102,147,187-102,147,187 View the variant detail on this assembly version. |
| hg38 | chr12:101,753,409-101,753,409 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_024312.4:c.3565C>T | NP_077288.2:p.Arg1189Ter |
| Ensemble | ENST00000299314.12:c.3565C>T | ENST00000299314.12:p.Arg1189Ter |
Summary
MGeND
| Clinical significance |
Likely pathogenic
Pathogenic
|
| Variant entry | 4 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:<0.001 |
| ToMMo:<0.001 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:<0.001 |
Prediction
ClinVar
| Clinical Significance |
Pathogenic
|
| Review star |  |
| Show details | |
Disease area statistics
MGeND
| Clinical significance | Last evaluated | Condition | Origin | Submission ID | Submitter | Institute | Citation | Comment | Image |
|---|---|---|---|---|---|---|---|---|---|
|
Pathogenic
|
other |
unknown
|
MGS000001
(TMGS000137) |
Kenjiro Kosaki | Keio University | ||||
|
Likely pathogenic
|
other |
unknown
|
MGS000001
(TMGS000137) |
Kenjiro Kosaki | Keio University | ||||
|
Likely pathogenic
|
other |
unknown
|
MGS000001
(TMGS000137) |
Kenjiro Kosaki | Keio University |
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Pathogenic
|
2020-09-16 | no assertion criteria provided | Mucolipidosis type II |
germline
unknown
|
Detail |
|
Pathogenic
|
2012-05-10 | no assertion criteria provided | Pseudo-Hurler polydystrophy |
germline
not provided
|
Detail |
|
Pathogenic
|
2024-01-31 | criteria provided, multiple submitters, no conflicts | Mucolipidosis type II,Pseudo-Hurler polydystrophy |
germline
unknown
|
Detail |
|
Pathogenic
|
2024-01-31 | criteria provided, multiple submitters, no conflicts | Mucolipidosis type II,Pseudo-Hurler polydystrophy |
germline
unknown
|
Detail |
|
Pathogenic
|
2018-09-10 | criteria provided, multiple submitters, no conflicts | not provided |
germline
|
Detail |
|
Pathogenic
|
2020-08-03 | criteria provided, single submitter | mucolipidosis |
germline
|
Detail |
|
Pathogenic
|
2023-11-10 | criteria provided, single submitter | GNPTAB-related disorder |
biparental
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.480 | Pseudo-Hurler polydystrophy | NA | CLINVAR | Detail | |
| 0.441 | MUCOLIPIDOSIS II ALPHA/BETA (disorder) | NA | CLINVAR | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_024312.5(GNPTAB):c.3565C>T (p.Arg1189Ter) AND Mucolipidosis type II | ClinVar | Detail |
| NM_024312.5(GNPTAB):c.3565C>T (p.Arg1189Ter) AND Pseudo-Hurler polydystrophy | ClinVar | Detail |
| NM_024312.5(GNPTAB):c.3565C>T (p.Arg1189Ter) AND multiple conditions | ClinVar | Detail |
| NM_024312.5(GNPTAB):c.3565C>T (p.Arg1189Ter) AND multiple conditions | ClinVar | Detail |
| NM_024312.5(GNPTAB):c.3565C>T (p.Arg1189Ter) AND not provided | ClinVar | Detail |
| NM_024312.5(GNPTAB):c.3565C>T (p.Arg1189Ter) AND Mucolipidosis | ClinVar | Detail |
| NM_024312.5(GNPTAB):c.3565C>T (p.Arg1189Ter) AND GNPTAB-related disorder | ClinVar | Detail |
| NA | 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
- rs137852897 dbSNP
- Genome
- hg38
- Position
- chr12:101,753,409-101,753,409
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- A
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1210
- Mean of sample read depth (HGVD)
- 109.39
- Standard deviation of sample read depth (HGVD)
- 48.87
- Number of reference allele (HGVD)
- 2418
- Number of alternative allele (HGVD)
- 1
- Allele Frequency (HGVD)
- 4.1339396444811904E-4
- Gene Symbol (HGVD)
- GNPTAB
- 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))
- rs137852897
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0004
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 7
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8654
- East Asian Allele Counts (ExAC)
- 2
- East Asian Heterozygous Counts (ExAC)
- 2
- East Asian Homozygous Counts (ExAC)
- 0
- East Asian Allele Frequency (ExAC)
- 2.3110700254217703E-4
- Chromosome Counts in All Race (ExAC)
- 121362
- Allele Counts in All Race (ExAC)
- 3
- Heterozygous Counts in All Race (ExAC)
- 3
- Homozygous Counts in All Race (ExAC)
- 0
- Allele Frequency in All Race (ExAC)
- 2.4719434419340485E-5
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