chr2:211540507:C>A Detail (hg19) (CPS1)

Information

Genome

Assembly Position
hg19 chr2:211,540,507-211,540,507
hg38 chr2:210,675,783-210,675,783 View the variant detail on this assembly version.

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
Links
Type Database ID Link
Gene MIM 608307 OMIM
HGNC 2323 HGNC
Ensembl ENSG00000021826 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv10356626 TogoVar
COSMIC
MONDO
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

DescrptionSourceLinks
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
hg19
Position
chr2:211,540,507-211,540,507
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
East Asian Homozygous Counts (ExAC)
118
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 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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