Search unique variants - LOVD - human mismatch repair genes

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Please note that this overview may not be complete, as variants with unknown effect to the phenotype are left out.

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The variants below are all in the MSH2 database, matching your query. 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 MSH2 full legend here.

33 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


1	c.6G>T	r.(?)	p.(=)	-	0.100	Class 2: Likely not pathogenic	Class 2: Likely not pathogenic	0.100	0.696	0.070	0.0077	Thompson et al., 2013	-	DNA	SEQ
1	c.23C>T	r.23c>u	p.Thr8Met	0.001	0.100	Class 1: Not pathogenic	Class 1: Not pathogenic	0.001	0.113	1.13E-04	1.26E-05	Thompson et al., 2014, InSiGHT	-	DNA	SEQ
2	c.279_281del	r.279_281del	p.Leu94del	-	0.604	Class 1: Not pathogenic	Class 1: Not pathogenic	0.010	0.065	0.001	0.0010	Thompson et al., 2014, InSiGHT	-	DNA	SEQ
2	c.287G>A	r.(?)	p.(Arg96His)	0.079	0.100	Class 2: Likely not pathogenic	Class 2: Likely not pathogenic	-	0.059	0.059	0.0065	Thompson et al., 2014, InSiGHT	-	DNA	SEQ
2	c.317G>A	r.(?)	p.(Arg106Lys)	1.74E-04	0.100	Class 1: Not pathogenic	Class 1: Not pathogenic	0.100	0.065	0.006	0.0007	Thompson et al., 2014, InSiGHT	-	DNA	SEQ
2	c.339G>A	r.339g>a	p.=	-	0.100	Class 1: Not pathogenic	Class 1: Not pathogenic	0.004	0.119	4.75E-04	0.0001	Thompson et al., 2013	-	DNA	SEQ
2	c.965G>A	r.965g>a	p.Gly322Asp	0.003	0.100	Class 1: Not pathogenic	Class 1: Not pathogenic	4.45E-13	1.023	4.56E-13	5.06E-14	Thompson et al., 2014, InSiGHT	-	DNA	SEQ
3	c.304G>A	r.[302_306del, 304g>a]	p.[Glu101Valfs*14, Glu102Lys]	0.013	0.100	Class 2: Likely not pathogenic	Class 2: Likely not pathogenic	0.040	-	0.040	0.0044	Thompson et al., 2014, InSiGHT	-	DNA	SEQ
3	c.505A>G	r.(?)	p.(Ile169Val)	0.002	0.100	Class 2: Likely not pathogenic	Class 2: Likely not pathogenic	0.866	0.068	0.059	0.0065	Thompson et al., 2014, InSiGHT	-	DNA	SEQ
3	c.593A>G	r.593a>g	p.Glu198Gly	0.934	0.900	Class 1: Not pathogenic	Class 1: Not pathogenic	6.40E-05	0.818	5.24E-05	0.0005	Thompson et al., 2014, InSiGHT	-	DNA	SEQ
3'UTR	c.*129T>C	r.(?)	p.(=)	-	0.260	Class 1: Not pathogenic	Class 1: Not pathogenic	0.003	0.793	0.002	0.0008	Thompson et al., 2013	-	DNA	SEQ
3'UTR	c.*221G>T	r.(?)	p.(=)	-	0.260	Class 2: Likely not pathogenic	Class 2: Likely not pathogenic	0.040	1.351	0.054	0.0186	Thompson et al., 2013	-	DNA	SEQ
3'UTR	c.*226A>G	r.(?)	p.(=)	0.897	0.260	Class 2: Likely not pathogenic	Class 2: Likely not pathogenic	0.080	-	0.080	0.0273	Thompson et al., 2013	-	DNA	SEQ
6	c.984C>T	r.(?)	p.(=)	-	0.100	Class 2: Likely not pathogenic	Class 2: Likely not pathogenic	0.346	-	0.346	0.0371	Thompson et al., 2014, InSiGHT	-	DNA	SEQ
6	c.991A>G	r.991a>g	p.Asn331Asp	0.757	0.757	Class 2: Likely not pathogenic	Class 2: Likely not pathogenic	0.040	0.400	0.016	0.0476	Thompson et al., 2014, InSiGHT	-	DNA	SEQ
7	c.1168C>T	r.1168c>u	p.Leu390Phe	0.112	0.112	Class 1: Not pathogenic	Class 1: Not pathogenic	1.55E-07	0.276	4.27E-08	5.40E-09	Thompson et al., 2014, InSiGHT	-	DNA	SEQ
7	c.1255C>A	r.(?)	p.(Gln419Lys)	0.002	0.100	Class 2: Likely not pathogenic	Class 2: Likely not pathogenic	0.035	-	0.035	0.0038	Thompson et al., 2014, InSiGHT	-	DNA	SEQ
8i	c.1387-8G>T	r.=	p.=	-	0.260	Class 2: Likely not pathogenic	Class 2: Likely not pathogenic	-	0.077	0.077	0.0264	Thompson et al., 2014, InSiGHT	-	DNA	SEQ
10i	c.1661+6C>T	r.=	p.=	-	0.260	Class 2: Likely not pathogenic	Class 2: Likely not pathogenic	0.100	-	0.100	0.0339	Thompson et al., 2014, InSiGHT	-	DNA	SEQ
10i	c.1662-9G>A	r.=	p.=	-	0.260	Class 1: Not pathogenic	Class 1: Not pathogenic	2.80E-12	-	2.80E-12	9.85E-13	Thompson et al., 2013	-	DNA	SEQ
11	c.1666T>C	r.1666u>c	p.=	-	0.100	Class 1: Not pathogenic	Class 1: Not pathogenic	5.86E-06	-	5.86E-06	1.00E-06	Thompson et al., 2013	-	DNA	SEQ
11	c.1690A>G	r.(=)	p.(Thr564Ala)	0.004	0.100	Class 1: Not pathogenic	Class 1: Not pathogenic	0.002	-	0.002	0.0002	Thompson et al., 2014, InSiGHT	-	DNA	SEQ
11	c.1730T>C	r.(?)	p.(Ile577Thr)	0.325	0.325	Class 2: Likely not pathogenic	Class 2: Likely not pathogenic	0.100	0.898	0.090	0.0414	Thompson et al., 2014, InSiGHT	-	DNA	SEQ
11	c.1737A>G	r.1737a>g	p.=	-	0.100	Class 2: Likely not pathogenic	Class 2: Likely not pathogenic	-	0.057	0.057	0.0063	Thompson et al., 2014, InSiGHT	-	DNA	SEQ
11	c.1755T>C	r.(?)	p.(=)	-	0.100	Class 2: Likely not pathogenic	Class 2: Likely not pathogenic	-	0.055	0.055	0.0061	Thompson et al., 2014, InSiGHT	-	DNA	SEQ
12	c.1886A>G	r.(?)	p.(Gln629Arg)	0.001	0.100	Class 1: Not pathogenic	Class 1: Not pathogenic	0.241	0.029	0.007	0.0008	Thompson et al., 2014, InSiGHT	-	DNA	SEQ
12	c.1963G>A	r.(?)	p.(Val655Ile)	0.000452	0.1	Class 2: Likely not pathogenic	Class 2: Likely not pathogenic	0.08	-	0.08	0.0088	InSiGHT	-	DNA	SEQ
12i	c.2005+8dup	r.=	p.=	-	0.260	Class 3: Uncertain	Class 2: Likely not pathogenic	1.840	-	1.840	0.3926	Thompson et al., 2013	-	DNA	SEQ
13	c.2154A>G	r.2154a>g	p.=	-	0.100	Class 2: Likely not pathogenic	Class 2: Likely not pathogenic	-	0.053	0.053	0.0058	Thompson et al., 2014, InSiGHT	-	DNA	SEQ
14	c.2437A>G	r.(?)	p.(Met813Val)	0.486	0.486	Class 2: Likely not pathogenic	Class 2: Likely not pathogenic	0.040	-	0.040	0.0365	Thompson et al., 2014, InSiGHT	-	DNA	SEQ
15	c.2500G>A	r.?	p.(Ala834Thr)	0.428	0.428	Class 2: Likely not pathogenic	Class 2: Likely not pathogenic	0.004	0.982	0.004	0.0029	Thompson et al., 2014, InSiGHT	-	DNA	SEQ
15	c.2579C>T	r.(?)	p.(Ser860Leu)	0.005	0.100	Class 2: Likely not pathogenic	Class 2: Likely not pathogenic	0.346	-	0.346	0.0371	Thompson et al., 2014, InSiGHT	-	DNA	SEQ
15	c.2583A>G	r.(?)	p.(=)	-	0.100	Class 2: Likely not pathogenic	Class 2: Likely not pathogenic	-	0.108	0.108	0.0118	Thompson et al., 2014, InSiGHT	-	DNA	SEQ

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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: [ MSH2 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.

LOVD - human mismatch repair genes

MutS homolog 2, ex-UVs (MSH2)