chr22:50625443:G>A Detail (hg38) (ARSA)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr22:51,063,871-51,063,871 View the variant detail on this assembly version. |
| hg38 | chr22:50,625,443-50,625,443 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_001085426.2:c.1232C>T | NP_001078895.2:p.Thr411Ile |
| NM_001085428.2:c.974C>T | NP_001078897.1:p.Thr325Ile | |
| NM_001085425.2:c.1232C>T | NP_001078894.2:p.Thr411Ile |
Summary
MGeND
| Clinical significance |
Pathogenic
|
| Variant entry | 2 |
| 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:[No Data.] |
Prediction
ClinVar
| Clinical Significance |
Pathogenic
Likely pathogenic
|
| Review star |  |
| Show details | |
Disease area statistics
MGeND
| Clinical significance | Last evaluated | Condition | Origin | Submission ID | Submitter | Institute | Citation | Comment | Image |
|---|---|---|---|---|---|---|---|---|---|
|
Pathogenic
|
juvenile metachromatic leukodystrophy with mental regression |
germline
|
MGS000082
(TMGS000165) |
Kenjiro Kosaki Kenjiro Kosaki |
Keio University Mutation View |
||||
|
Pathogenic
|
Adult type |
germline
|
MGS000001
(TMGS000178) |
Kenjiro Kosaki | Keio University |
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Pathogenic
|
1994-04-01 | no assertion criteria provided | Metachromatic leukodystrophy, mild |
germline
|
Detail |
|
Pathogenic
Likely pathogenic
|
2023-08-10 | criteria provided, multiple submitters, no conflicts | metachromatic leukodystrophy |
germline
unknown
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.514 | Leukodystrophy, Metachromatic | NA | CLINVAR | Detail | |
| 0.514 | Leukodystrophy, Metachromatic | She was diagnosed with MLD by genetic analysis, which revealed compound heterozy... | UNIPROT | 21265945 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_000487.6(ARSA):c.1232C>T (p.Thr411Ile) AND Metachromatic leukodystrophy, mild | ClinVar | Detail |
| NM_000487.6(ARSA):c.1232C>T (p.Thr411Ile) AND Metachromatic leukodystrophy | ClinVar | Detail |
| NA | DisGeNET | Detail |
| She was diagnosed with MLD by genetic analysis, which revealed compound heterozygous ARSA missense m... | 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
- rs74315481 dbSNP
- Genome
- hg38
- Position
- chr22:50,625,443-50,625,443
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- A
- Filtering Status (HGVD)
- PASS
- Filtering Status (HGVD)
- LowQual
- # of samples (HGVD)
- 1201
- Mean of sample read depth (HGVD)
- 46.51
- Standard deviation of sample read depth (HGVD)
- 22.25
- Number of reference allele (HGVD)
- 2401
- Number of alternative allele (HGVD)
- 1
- Allele Frequency (HGVD)
- 4.1631973355537054E-4
- Gene Symbol (HGVD)
- ARSA
- 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))
- rs74315481
- 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))
- 6
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
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