CPS1 T1406N - GET-Evidence

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Note: This variant has not been sufficiently evaluated by a GET-Evidence editor.

To be considered sufficiently evaluated a variant must have both "variant evidence" and "clinical importance" scores filled in.

Please help improve GET-Evidence by evaluating evidence for this variant!

Curation:
Currentness:

(See the latest version)

CPS1 T1406N

(CPS1 Thr1406Asn)


You are viewing an old version of this page that was saved on November 29, 2012 at 5:18am by Genome Importing Robot.

Short summary

 

Variant evidence
Computational 3

PolyPhen2: Benign, score 0.005
SIFT: Affect protein function 0.00
GVGD: GV 0.00; GD 64.77; Class C55
Variant Effect Predictor (Ensembl):
SIFT=tolerated(0.15);
PolyPhen=benign(0.005);
Condel=deleterious(0.784)
Mutation Tasting Prediction: Polymorphism, P value: 0.719730
protein features (might be) affected (aa 1406-1408 STRAND gets lost)

Functional -
Case/Control -
Familial -
 
Clinical importance
Severity -
Treatability -
Penetrance -
 

Impact

Insufficiently evaluated not reviewed

(The "insufficiently evaluated" qualifier is assigned automatically based on the above evidence and importance scores.)

Inheritance pattern

unknown

Summary of published research, and additional commentary

 

Allele frequency

  • A @ chr2:211540507: 32.9% (3543/10758) in EVS
  • A @ chr2:211248751: 26.6% (33/124) in GET-Evidence
  • Frequency shown in summary reports: 32.9% (3543/10758)

Publications
 

Genomes
 

hu0D879F - CGI sample GS00253-DNA_G01_200_37
het A @ chr2:211540507

 

hu0E64A1 - CGI sample GS01173-DNA_B02 from PGP sample 94378523
het A @ chr2:211540507

 

Added in this revision:

hu241DEA - CGI sample GS01175-DNA_D05 from PGP sample 1205491
het A @ chr2:211540507

 

hu2D6140 - CGI sample GS01173-DNA_F06 from PGP sample 64191565
het A @ chr2:211540507

 

hu3215A7 - PGP12 (hu3215A7) build 36, substitution variants, hu3215A7 build 36 substitution variants
het A @ chr2:211248752

 

hu34D5B9 - CGI sample GS01173-DNA_C07 from PGP sample 92161424, hu34D5B9 exome
het A @ chr2:211540507

 

hu6E4515 - PGP15 (hu6E4515) build 37, from CGI var (software ver 1.12.0.47), CGI sample GS000005532
het A @ chr2:211540507

 

hu728FFF - PGP11 (hu728FFF) build 36, substitution variants, hu728FFF build 36 substitution variants
het A @ chr2:211248752

 

hu72A81D - CGI sample GS01173-DNA_C02 from PGP sample 10366372
het A @ chr2:211540507

 

hu8229AE - CGI sample GS01173-DNA_A07 from PGP sample 96240009
het A @ chr2:211540507

 

huA0E089 - CGI sample GS01175-DNA_B04 from PGP sample 88590671
het A @ chr2:211540507

 

huA90CE6 - PGP16 (huA90CE6) build 37, from CGI var (software ver 2.0.2.11), CGI sample GS000006909
het A @ chr2:211540507

 

huBAAC98 - CGI sample GS01173-DNA_F02 from PGP sample 70008981
het A @ chr2:211540507

 

huC30901 - CGI sample GS00253-DNA_B01_200_37
hom A @ chr2:211540507

 

huCA017E - CGI sample GS01175-DNA_B01 from PGP sample 86206034
het A @ chr2:211540507

 

huE80E3D - CGI sample GS00253-DNA_D01_200_37
het A @ chr2:211540507

 

huFAF983 - CGI sample GS01175-DNA_F02 from PGP sample 95788191
hom A @ chr2:211540507

 

GS10851 - var-GS10851-1100-36-ASM
hom A @ chr2:211248752

 

GS18501 - var-GS18501-1100-36-ASM
het A @ chr2:211248752

 

GS18504 - var-GS18504-1100-36-ASM
het A @ chr2:211248752

 

GS18517 - var-GS18517-1100-36-ASM
het A @ chr2:211248752

 

GS18558 - var-GS18558-1100-36-ASM
het A @ chr2:211248752

 

GS18942 - var-GS18942-1100-36-ASM
het A @ chr2:211248752

 

GS18947 - var-GS18947-1100-36-ASM
het A @ chr2:211248752

 

GS18956 - var-GS18956-1100-36-ASM
het A @ chr2:211248752

 

GS19026 - var-GS19026-1100-36-ASM
hom A @ chr2:211248752

 

GS19129 - var-GS19129-1100-36-ASM
het A @ chr2:211248752

 

GS19238 - var-GS19238-1100-36-ASM
het A @ chr2:211248752

 

GS19649 - var-GS19649-1100-36-ASM
het A @ chr2:211248752

 

GS19670 - var-GS19670-1100-36-ASM
het A @ chr2:211248752

 

GS19700 - var-GS19700-1100-36-ASM
het A @ chr2:211248752

 

GS20502 - var-GS20502-1100-36-ASM
het A @ chr2:211248752

 

GS20509 - var-GS20509-1100-36-ASM
hom A @ chr2:211248752

 

GS21767 - var-GS21767-1100-36-ASM
het A @ chr2:211248752

 

Other external references
 

    dbSNP
  • rs1047891
    www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi
    GeneTests
  • GeneTests records for the CPS1 gene
    21-Hydroxylase-Deficient Congenital Adrenal Hyperplasia
    Carbamoylphosphate Synthetase I Deficiency
    www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/CPS1
    PolyPhen-2
  • Score: 0 (benign)
    Web search results (2 hits -- see all)
  • Gene Structure of Human Carbamylphosphate Synthetase 1 and ...
    genomic structure of the CPS1 gene was not yet elucidated, mutation detection was ... in family 5, both parents were heterozygous for the T1406N polymorphism while the patient ...
    interscience.wiley.com/homepages/38515/pdf/mutation/589.pdf
  • Supplementary Table xls.1
    Administrator B**a***=***£***h*J*\I08*X*@*ì*"*******1* É*ÿ**Arial1* É*ÿ ... "ú"#,##0;\-"ú"#,##0*"ú"#,##0;[Red]\-"ú"#,##0*"ú"#,##0.00;\-"ú"#,##0.00**#*"ú" ...
    icr.ac.uk/research/research_sections/.../2843.xls

Other in silico analyses
 

  • NBLOSUM100 score = 1
  • GET-Evidence autoscore = 3

Edit history
 

Gene search

"GENE" or "GENE A123C":

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