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NM_000179.3(MSH6):c.3801+2T>C AND Lynch syndrome

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
May 1, 2018
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000758619.3

Allele description [Variation Report for NM_000179.3(MSH6):c.3801+2T>C]

NM_000179.3(MSH6):c.3801+2T>C

Gene:
MSH6:mutS homolog 6 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2p16.3
Genomic location:
Preferred name:
NM_000179.3(MSH6):c.3801+2T>C
HGVS:
  • NC_000002.12:g.47806360T>C
  • NG_007111.1:g.28214T>C
  • NG_008397.1:g.104316A>G
  • NM_000179.3:c.3801+2T>CMANE SELECT
  • NM_001281492.2:c.3411+2T>C
  • NM_001281493.2:c.2895+2T>C
  • NM_001281494.2:c.2895+2T>C
  • NM_001406795.1:c.3897+2T>C
  • NM_001406796.1:c.3801+2T>C
  • NM_001406797.1:c.3504+2T>C
  • NM_001406798.1:c.3627+2T>C
  • NM_001406799.1:c.3276+2T>C
  • NM_001406800.1:c.3801+2T>C
  • NM_001406801.1:c.3504+2T>C
  • NM_001406802.1:c.3897+2T>C
  • NM_001406803.1:c.2937+2T>C
  • NM_001406804.1:c.3723+2T>C
  • NM_001406805.1:c.3504+2T>C
  • NM_001406806.1:c.3276+2T>C
  • NM_001406807.1:c.3276+2T>C
  • NM_001406808.1:c.3801+2T>C
  • NM_001406809.1:c.3801+2T>C
  • NM_001406811.1:c.2895+2T>C
  • NM_001406812.1:c.2895+2T>C
  • NM_001406813.1:c.3807+2T>C
  • NM_001406814.1:c.2895+2T>C
  • NM_001406815.1:c.2895+2T>C
  • NM_001406816.1:c.2895+2T>C
  • NM_001406817.1:c.2235+2T>C
  • NM_001406818.1:c.3504+2T>C
  • NM_001406819.1:c.3504+2T>C
  • NM_001406820.1:c.3504+2T>C
  • NM_001406821.1:c.3504+2T>C
  • NM_001406822.1:c.3504+2T>C
  • NM_001406823.1:c.2895+2T>C
  • NM_001406824.1:c.3504+2T>C
  • NM_001406825.1:c.3504+2T>C
  • NM_001406826.1:c.3633+2T>C
  • NM_001406827.1:c.3504+2T>C
  • NM_001406828.1:c.3504+2T>C
  • NM_001406829.1:c.2895+2T>C
  • NM_001406830.1:c.3504+2T>C
  • NM_001406831.1:c.582+2T>C
  • NM_001406832.1:c.648+2T>C
  • NM_001407362.1:c.1746+2T>C
  • LRG_219t1:c.3801+2T>C
  • LRG_219:g.28214T>C
  • NC_000002.11:g.48033499T>C
  • NM_000179.2:c.3801+2T>C
Links:
dbSNP: rs1558392617
NCBI 1000 Genomes Browser:
rs1558392617
Molecular consequence:
  • NM_000179.3:c.3801+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001281492.2:c.3411+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001281493.2:c.2895+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001281494.2:c.2895+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406795.1:c.3897+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406796.1:c.3801+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406797.1:c.3504+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406798.1:c.3627+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406799.1:c.3276+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406800.1:c.3801+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406801.1:c.3504+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406802.1:c.3897+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406803.1:c.2937+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406804.1:c.3723+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406805.1:c.3504+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406806.1:c.3276+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406807.1:c.3276+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406808.1:c.3801+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406809.1:c.3801+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406811.1:c.2895+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406812.1:c.2895+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406813.1:c.3807+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406814.1:c.2895+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406815.1:c.2895+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406816.1:c.2895+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406817.1:c.2235+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406818.1:c.3504+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406819.1:c.3504+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406820.1:c.3504+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406821.1:c.3504+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406822.1:c.3504+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406823.1:c.2895+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406824.1:c.3504+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406825.1:c.3504+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406826.1:c.3633+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406827.1:c.3504+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406828.1:c.3504+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406829.1:c.2895+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406830.1:c.3504+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406831.1:c.582+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406832.1:c.648+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001407362.1:c.1746+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:
Lynch syndrome
Identifiers:
MONDO: MONDO:0005835; MedGen: C4552100

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000887376University of Washington Department of Laboratory Medicine, University of Washington
criteria provided, single submitter

(Shirts BH et al. (Am J Hum Genet 2018))		Likely pathogenic
(May 1, 2018) 		somaticclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedsomaticyesnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Using Somatic Mutations from Tumors to Classify Variants in Mismatch Repair Genes.

Shirts BH, Konnick EQ, Upham S, Walsh T, Ranola JMO, Jacobson AL, King MC, Pearlman R, Hampel H, Pritchard CC.

Am J Hum Genet. 2018 Jul 5;103(1):19-29. doi: 10.1016/j.ajhg.2018.05.001. Epub 2018 Jun 7.

PubMed [citation]
PMID:
29887214
PMCID:
PMC6035155

Details of each submission

From University of Washington Department of Laboratory Medicine, University of Washington, SCV000887376.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

MSH6 NM_000179.2:c.3801+2T>C has a 98.1% probability of pathogenicity based on combining prior probability from public data with a likelihood ratio of 1.56 to 1, generated from evidence of seeing this as a somatic mutation in a tumor without loss of heterozygosity at the MSH6 locus. See Shirts et al 2018, PMID 29887214.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1somaticyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 1, 2024