chr2:210675783:C>A Detail (hg38) (CPS1)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr2:211,540,507-211,540,507 View the variant detail on this assembly version. |
| hg38 | chr2:210,675,783-210,675,783 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_001875.4:c.4217C>A | NP_001866.2:p.Thr1406Asn |
| NM_001122633.2:c.4235C>A | NP_001116105.1:p.Thr1412Asn | |
| NM_001122634.3:c.2864C>A | NP_001116106.1:p.Thr955Asn |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.158 |
| ToMMo:0.154 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.167 |
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 |
|---|---|---|---|---|---|
|
Benign
|
2013-06-18 | criteria provided, multiple submitters, no conflicts | not specified |
germline
|
Detail |
|
Benign
|
2024-02-01 | criteria provided, multiple submitters, no conflicts | Congenital hyperammonemia, type I |
germline
|
Detail |
risk factor
|
2011-09-01 | no assertion criteria provided | Pulmonary hypertension, neonatal, susceptibility to |
germline
|
Detail |
|
Benign
|
2011-09-01 | no assertion criteria provided | CARBAMOYL PHOSPHATE SYNTHETASE I POLYMORPHISM |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.006 | Necrotizing Enterocolitis | These data suggest that the CPS1 T1405N polymorphism may be associated with the ... | BeFree | 17597649 | Detail |
| 0.122 | Fibrinogen Adverse Event | [A genome-wide survey of the human genome identifies novel loci related to commo... | GAD | 20031577 | Detail |
| <0.001 | Down syndrome | Unconditional logistic regression analysis of the modeling cohort revealed that ... | BeFree | 17188582 | Detail |
| 0.003 | pulmonary hypertension | A well-characterized polymorphism in the gene encoding CPSI (T1405N) has previou... | BeFree | 17188582 | Detail |
| <0.001 | Cardiac defects | In conclusion, the CPSI T1405N genotype appears to be an important new factor in... | BeFree | 17188582 | Detail |
| 0.002 | Creatinine finding | [New loci associated with kidney function and chronic kidney disease.] | GAD | 20383146 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_001875.5(CPS1):c.4217C>A (p.Thr1406Asn) AND not specified | ClinVar | Detail |
| NM_001875.5(CPS1):c.4217C>A (p.Thr1406Asn) AND Congenital hyperammonemia, type I | ClinVar | Detail |
| NM_001875.5(CPS1):c.4217C>A (p.Thr1406Asn) AND Pulmonary hypertension, neonatal, susceptibility to | ClinVar | Detail |
| NM_001875.5(CPS1):c.4217C>A (p.Thr1406Asn) AND CARBAMOYL PHOSPHATE SYNTHETASE I POLYMORPHISM | ClinVar | Detail |
| These data suggest that the CPS1 T1405N polymorphism may be associated with the risk of NEC in prete... | DisGeNET | Detail |
| [A genome-wide survey of the human genome identifies novel loci related to common chronic inflammato... | DisGeNET | Detail |
| Unconditional logistic regression analysis of the modeling cohort revealed that age (OR=0.92, p=0.01... | DisGeNET | Detail |
| A well-characterized polymorphism in the gene encoding CPSI (T1405N) has previously been implicated ... | DisGeNET | Detail |
| In conclusion, the CPSI T1405N genotype appears to be an important new factor in predicting suscepti... | DisGeNET | Detail |
| [New loci associated with kidney function and chronic kidney disease.] | 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
- rs1047891 dbSNP
- Genome
- hg38
- Position
- chr2:210,675,783-210,675,783
- Variant Type
- snv
- Reference Allele
- C
- Alternative Allele
- A
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1189
- Mean of sample read depth (HGVD)
- 87.96
- Standard deviation of sample read depth (HGVD)
- 39.15
- Number of reference allele (HGVD)
- 2003
- Number of alternative allele (HGVD)
- 375
- Allele Frequency (HGVD)
- 0.1576955424726661
- Gene Symbol (HGVD)
- CPS1
- 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))
- rs1047891
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.1545
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 2590
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8646
- East Asian Allele Counts (ExAC)
- 1447
- East Asian Heterozygous Counts (ExAC)
- 1211
- East Asian Homozygous Counts (ExAC)
- 118
- East Asian Allele Frequency (ExAC)
- 0.16736062919269026
- Chromosome Counts in All Race (ExAC)
- 121204
- Allele Counts in All Race (ExAC)
- 36772
- Heterozygous Counts in All Race (ExAC)
- 25388
- Homozygous Counts in All Race (ExAC)
- 5692
- Allele Frequency in All Race (ExAC)
- 0.3033893270849147
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