PMS2 K541E - GET-Evidence

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)

PMS2 K541E

(PMS2 Lys541Glu)


You are viewing an old version of this page that was saved on November 29, 2012 at 3:55am by Genome Importing Robot.

Short summary

 

Variant evidence
Computational 4

Variant Effect Predictor (Ensembl ):
SIFT=tolerated(0.96);
PolyPhen=benign(0)
Mutation Tasting prediction: Polymorphism p value: 0.999932; no protein features affected.
GVGD: GV 101.46; GD 0.00; Class C0
Multi-alignment of P54278.2 Mismatch repair endonuclease [Homo sapiens] with: XP_001141671.1 [Pan troglodytes] XP_002806632.1 [Callithrix jacchus] XP_001494013.1 [Equus caballus] XP_002817725.1 [Pongo abelii] NP_001192867.1 [Bos taurus] XP_002927619.1 [Ailuropoda melanoleuca] NP_032912.2 [Mus musculus] BAE27115.1 [Mus musculus] EDL19031.1 [Mus musculus] XP_536879.2 [Canis familiaris]

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

  • C @ chr7:6026775: 87.4% (9396/10752) in EVS
  • C @ chr7:5993300: 89.7% (113/126) in GET-Evidence
  • Frequency shown in summary reports: 87.4% (9396/10752)

Publications
 

Genomes
 

hu034DB1 - CGI sample GS00253-DNA_A02_200_37
hom C @ chr7:6026775

 

hu04FD18 - CGI sample GS00253-DNA_F01_200_37
hom C @ chr7:6026775

 

hu0D879F - CGI sample GS00253-DNA_G01_200_37
hom C @ chr7:6026775

 

 

 

 

 

 

 

 

 

hu43860C - CGI sample GS00253-DNA_A01_200_37
het C @ chr7:6026775

 

hu604D39 - CGI sample GS00253-DNA_B02_200_37
het C @ chr7:6026775

 

 

 

 

 

hu9385BA - CGI sample GS00253-DNA_E01_200_37
hom C @ chr7:6026775

 

 

huAE6220 - CGI sample GS00253-DNA_H01_200_37
hom C @ chr7:6026775

 

 

 

huBEDA0B - CGI sample GS00253-DNA_C01_200_37
hom C @ chr7:6026775

 

Added in this revision:

 

 

huE80E3D - CGI sample GS00253-DNA_D01_200_37
hom C @ chr7:6026775

 

GS06985 - var-GS06985-1100-36-ASM
hom C @ chr7:5993301

 

GS06994 - var-GS06994-1100-36-ASM
hom C @ chr7:5993301

 

GS07357 - var-GS07357-1100-36-ASM
het C @ chr7:5993301

 

GS10851 - var-GS10851-1100-36-ASM
hom C @ chr7:5993301

 

GS12004 - var-GS12004-1100-36-ASM
hom C @ chr7:5993301

 

GS18501 - var-GS18501-1100-36-ASM
hom C @ chr7:5993301

 

GS18502 - var-GS18502-1100-36-ASM
hom C @ chr7:5993301

 

GS18504 - var-GS18504-1100-36-ASM
hom C @ chr7:5993301

 

GS18505 - var-GS18505-1100-36-ASM
het C @ chr7:5993301

 

GS18508 - var-GS18508-1100-36-ASM
hom C @ chr7:5993301

 

GS18517 - var-GS18517-1100-36-ASM
hom C @ chr7:5993301

 

GS18526 - var-GS18526-1100-36-ASM
hom C @ chr7:5993301

 

GS18537 - var-GS18537-1100-36-ASM
hom C @ chr7:5993301

 

GS18555 - var-GS18555-1100-36-ASM
hom C @ chr7:5993301

 

GS18558 - var-GS18558-1100-36-ASM
hom C @ chr7:5993301

 

GS18940 - var-GS18940-1100-36-ASM
hom C @ chr7:5993301

 

GS18942 - var-GS18942-1100-36-ASM
hom C @ chr7:5993301

 

GS18947 - var-GS18947-1100-36-ASM
hom C @ chr7:5993301

 

GS18956 - var-GS18956-1100-36-ASM
hom C @ chr7:5993301

 

GS19020 - var-GS19020-1100-36-ASM
hom C @ chr7:5993301

 

GS19025 - var-GS19025-1100-36-ASM
hom C @ chr7:5993301

 

GS19026 - var-GS19026-1100-36-ASM
hom C @ chr7:5993301

 

GS19129 - var-GS19129-1100-36-ASM
hom C @ chr7:5993301

 

GS19238 - var-GS19238-1100-36-ASM
hom C @ chr7:5993301

 

GS19239 - var-GS19239-1100-36-ASM
hom C @ chr7:5993301

 

GS19240 - var-GS19240-1100-36-ASM
hom C @ chr7:5993301

 

GS19648 - var-GS19648-1100-36-ASM
hom C @ chr7:5993301

 

GS19649 - var-GS19649-1100-36-ASM
hom C @ chr7:5993301

 

GS19669 - var-GS19669-1100-36-ASM
het C @ chr7:5993301

 

GS19670 - var-GS19670-1100-36-ASM
het C @ chr7:5993301

 

GS19700 - var-GS19700-1100-36-ASM
hom C @ chr7:5993301

 

GS19701 - var-GS19701-1100-36-ASM
hom C @ chr7:5993301

 

GS19703 - var-GS19703-1100-36-ASM
hom C @ chr7:5993301

 

GS19704 - var-GS19704-1100-36-ASM
hom C @ chr7:5993301

 

GS19735 - var-GS19735-1100-36-ASM
het C @ chr7:5993301

 

GS19834 - var-GS19834-1100-36-ASM
hom C @ chr7:5993301

 

GS20502 - var-GS20502-1100-36-ASM
hom C @ chr7:5993301

 

GS20509 - var-GS20509-1100-36-ASM
hom C @ chr7:5993301

 

GS21767 - var-GS21767-1100-36-ASM
het C @ chr7:5993301

 

Other external references
 

    dbSNP
  • rs41534544
    www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi
  • rs2228006
    www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi
    GeneTests
  • GeneTests records for the PMS2 gene
    Turcot Syndrome
    Hereditary Non-Polyposis Colon Cancer
    PMS2-Related Hereditary Non-Polyposis Colon Cancer
    PMS2-Related Turcot Syndrome
    www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/PMS2
    Web search results (0 hits -- see all)

Other in silico analyses
 

  • NBLOSUM100 score = 0
  • GET-Evidence autoscore = 2

Edit history
 

Gene search

"GENE" or "GENE A123C":

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