View unique variants - LOVD - human mismatch repair genes

Batch queries can be done using pipe "|" as a separator between search terms.

About this overview [Show]

The variants below are all in the PMS2 database. In this view only variant fields are shown. Variants are listed only once, a number is present in the DNA change field when a variant has been reported more than once (in such cases fields other than the DNA change just belong to one entry and may differ for other entries).
Selecting and clicking a specific line will open a detailed view showing all variant entries, including patient and pathogenicity information.
At the bottom of this page a legend is provided with a short explanation of what each field contains.
For a more detailed description of each field, please see the PMS2 full legend here.

8 entries
entries per page

Exon

DNA change

RNA change

Protein

MAPP/PP2 Prior P

Prior P

IARC Classification

InSiGHT Classification

Tumour Char LR

Segregation LR

Odds for causality

Posterior P

Reference

Variant remarks

Template

Technique

DB-ID


2	c.52A>G	r.(?)	p.(Ile18Val)	0.557	0.557	Class 3: Uncertain	Class 3: Uncertain	-	0.081	0.081	0.0920	Thompson et al., 2014, InSiGHT	-	DNA	SEQ	PMS2_00001
2	c.137G>T	r.(?)	p.(Ser46Ile)	0.939	0.900	Class 3: Uncertain	Class 4: Likely pathogenic	0.100	6.221	0.622	0.8485	Thompson et al., 2014, InSiGHT	-	DNA	SEQ	PMS2_00002
3	c.180C>G	r.(?)	p.(Asp60Glu)	4.05E-04	0.100	Class 2: Likely not pathogenic	Class 2: Likely not pathogenic	0.100	0.164	0.016	0.0018	Thompson et al., 2014, InSiGHT	-	DNA	SEQ	PMS2_00003
3i	c.251-8T>C	r.(?)	p.(=)	-	0.260	Class 3: Uncertain	Class 3: Uncertain	-	0.279	0.279	0.0894	Thompson et al., 2014, InSiGHT	-	DNA	SEQ	PMS2_00007
10i	c.1144+2T>A	r.989_1144del	p.(Glu330_Glu381del)	-	0.960	Class 4: Likely pathogenic	Class 4: Likely pathogenic	-	2.777	2.777	0.9852	Thompson et al., 2014, InSiGHT	-	DNA	SEQ	PMS2_00008
11	c.1688G>T	r.(?)	p.(Arg563Leu)	0.001	0.100	Class 2: Likely not pathogenic	Class 2: Likely not pathogenic	-	0.021	0.021	0.0023	Thompson et al., 2014, InSiGHT	-	DNA	SEQ	PMS2_00004
11	c.1789A>T	r.1789a>u	p.Thr597Ser	3.54E-04	0.100	Class 2: Likely not pathogenic	Class 1: Not pathogenic	0.135	1.000	0.135	0.0148	Thompson et al., 2014, InSiGHT	-	DNA	SEQ	PMS2_00005
15	c.2528G>A	r.(?)	p.(Cys843Tyr)	0.879	0.879	Class 3: Uncertain	Class 3: Uncertain	-	0.279	0.279	0.6699	Thompson et al., 2014, InSiGHT	-	DNA	SEQ	PMS2_00006

1 - 8

Click here to save this list in a tab-delimited text file.

Note: Direct classification on the basis of the prior probability alone is a misuse of the Bayesian integrated evaluation model, therefore the dynamic range of the prior probability (Prior P) has been truncated to a minimum of 0.10 and a maximum of 0.90 so that additional sources of information are required to reach posterior probabilities that alter clinical management of patients with variants.

Legend: [ PMS2 full legend ]
Sequence variations are described basically as recommended by the Ad-Hoc Committee for Mutation Nomenclature (AHCMN), with the recently suggested additions (den Dunnen JT and Antonarakis SE [2000], Hum.Mut. 15:7-12); for a summary see Nomenclature.
Exon: Exon numbering. DNA change: Variation at DNA-level. If present, "Full Details" will show you the the full-length entry. RNA change: Variation at RNA-level, (?) unknown but probably identical to DNA. Protein: Variation at protein level. MAPP/PP2 Prior P: MAPP/PP2 Prior probability of pathogenicity Prior P: Prior probability of pathogenicity (used in Bayes Integrated Evaluation/Multifactorial Likelihood Analysis) IARC Classification: IARC Classification InSiGHT Classification: 5-tiered classification on the InSiGHT database Tumour Char LR: Tumour characteristics likelihood ratio Segregation LR: Segregation likelihood ratio Odds for causality: Product of LRs Posterior P: Posterior probability of pathogenicity Reference: Reference describing the variation, "Submitted:" indicating that the mutation was submitted directly to this database. Variant remarks: Variant remarks Template: Variant detected in DNA, RNA and/or Protein. Technique: Technique used to detect the variation. PMS2 DB-ID: Database IDentifier; When available, links to OMIM ID's are provided.

LOVD - human mismatch repair genes

Postmeiotic segregation increased 2, ex-UVs (PMS2)