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NM_000179.3(MSH6):c.3609_3612del (p.His1203fs) AND Hereditary nonpolyposis colorectal neoplasms

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 1, 2022
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:
RCV002514332.3

Allele description [Variation Report for NM_000179.3(MSH6):c.3609_3612del (p.His1203fs)]

NM_000179.3(MSH6):c.3609_3612del (p.His1203fs)

Gene:
MSH6:mutS homolog 6 [Gene - OMIM - HGNC]
Variant type:
Microsatellite
Cytogenetic location:
2p16.3
Genomic location:
Preferred name:
NM_000179.3(MSH6):c.3609_3612del (p.His1203fs)
HGVS:
  • NC_000002.12:g.47805666TGCA[1]
  • NG_007111.1:g.27520TGCA[1]
  • NG_008397.1:g.105005CATG[1]
  • NM_000179.3:c.3609_3612delMANE SELECT
  • NM_001281492.2:c.3219_3222del
  • NM_001281493.2:c.2703_2706del
  • NM_001281494.2:c.2703_2706del
  • NM_001406795.1:c.3705_3708del
  • NM_001406796.1:c.3609_3612del
  • NM_001406797.1:c.3312_3315del
  • NM_001406798.1:c.3435_3438del
  • NM_001406799.1:c.3084_3087del
  • NM_001406800.1:c.3609_3612del
  • NM_001406801.1:c.3312_3315del
  • NM_001406802.1:c.3705_3708del
  • NM_001406803.1:c.2745_2748del
  • NM_001406804.1:c.3531_3534del
  • NM_001406805.1:c.3312_3315del
  • NM_001406806.1:c.3084_3087del
  • NM_001406807.1:c.3084_3087del
  • NM_001406808.1:c.3609_3612del
  • NM_001406809.1:c.3609_3612del
  • NM_001406811.1:c.2703_2706del
  • NM_001406812.1:c.2703_2706del
  • NM_001406813.1:c.3615_3618del
  • NM_001406814.1:c.2703_2706del
  • NM_001406815.1:c.2703_2706del
  • NM_001406816.1:c.2703_2706del
  • NM_001406817.1:c.2043_2046del
  • NM_001406818.1:c.3312_3315del
  • NM_001406819.1:c.3312_3315del
  • NM_001406820.1:c.3312_3315del
  • NM_001406821.1:c.3312_3315del
  • NM_001406822.1:c.3312_3315del
  • NM_001406823.1:c.2703_2706del
  • NM_001406824.1:c.3312_3315del
  • NM_001406825.1:c.3312_3315del
  • NM_001406826.1:c.3441_3444del
  • NM_001406827.1:c.3312_3315del
  • NM_001406828.1:c.3312_3315del
  • NM_001406829.1:c.2703_2706del
  • NM_001406830.1:c.3312_3315del
  • NM_001406831.1:c.390_393del
  • NM_001406832.1:c.456_459del
  • NM_001407362.1:c.1554_1557del
  • NP_000170.1:p.His1203Glnfs
  • NP_000170.1:p.His1203fs
  • NP_001268421.1:p.His1073fs
  • NP_001268422.1:p.His901fs
  • NP_001268423.1:p.His901fs
  • NP_001393724.1:p.His1235fs
  • NP_001393725.1:p.His1203fs
  • NP_001393726.1:p.His1104fs
  • NP_001393727.1:p.His1145fs
  • NP_001393728.1:p.His1028fs
  • NP_001393729.1:p.His1203fs
  • NP_001393730.1:p.His1104fs
  • NP_001393731.1:p.His1235fs
  • NP_001393732.1:p.His915fs
  • NP_001393733.1:p.His1177fs
  • NP_001393734.1:p.His1104fs
  • NP_001393735.1:p.His1028fs
  • NP_001393736.1:p.His1028fs
  • NP_001393737.1:p.His1203fs
  • NP_001393738.1:p.His1203fs
  • NP_001393740.1:p.His901fs
  • NP_001393741.1:p.His901fs
  • NP_001393742.1:p.His1205fs
  • NP_001393743.1:p.His901fs
  • NP_001393744.1:p.His901fs
  • NP_001393745.1:p.His901fs
  • NP_001393746.1:p.His681fs
  • NP_001393747.1:p.His1104fs
  • NP_001393748.1:p.His1104fs
  • NP_001393749.1:p.His1104fs
  • NP_001393750.1:p.His1104fs
  • NP_001393751.1:p.His1104fs
  • NP_001393752.1:p.His901fs
  • NP_001393753.1:p.His1104fs
  • NP_001393754.1:p.His1104fs
  • NP_001393755.1:p.His1147fs
  • NP_001393756.1:p.His1104fs
  • NP_001393757.1:p.His1104fs
  • NP_001393758.1:p.His901fs
  • NP_001393759.1:p.His1104fs
  • NP_001393760.1:p.His130fs
  • NP_001393761.1:p.His152fs
  • NP_001394291.1:p.His518fs
  • LRG_219t1:c.3609_3612del
  • LRG_219:g.27520TGCA[1]
  • NC_000002.11:g.48032803_48032806del
  • NC_000002.11:g.48032805TGCA[1]
  • NM_000179.2:c.3605_3608TGCA[1]
  • NM_000179.2:c.3609_3612delTGCA
  • NM_000179.3:c.3609_3612delTGCAMANE SELECT
  • NR_176256.1:n.2535TGCA[1]
  • NR_176257.1:n.3866TGCA[1]
  • NR_176258.1:n.3795TGCA[1]
  • NR_176259.1:n.3694TGCA[1]
  • NR_176260.1:n.1639_1642TGCA[1]
  • NR_176261.1:n.3576TGCA[1]
Note:
NCBI staff could not confirm the published nucleotide change on the current reference sequence after review of PubMed 16283678.
Protein change:
H1028fs
Links:
OMIM: 600678.0013; dbSNP: rs587779274
NCBI 1000 Genomes Browser:
rs587779274
Molecular consequence:
  • NM_000179.3:c.3609_3612del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001281492.2:c.3219_3222del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001281493.2:c.2703_2706del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001281494.2:c.2703_2706del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406795.1:c.3705_3708del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406796.1:c.3609_3612del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406797.1:c.3312_3315del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406798.1:c.3435_3438del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406799.1:c.3084_3087del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406800.1:c.3609_3612del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406801.1:c.3312_3315del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406802.1:c.3705_3708del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406803.1:c.2745_2748del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406804.1:c.3531_3534del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406805.1:c.3312_3315del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406806.1:c.3084_3087del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406807.1:c.3084_3087del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406808.1:c.3609_3612del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406809.1:c.3609_3612del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406811.1:c.2703_2706del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406812.1:c.2703_2706del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406813.1:c.3615_3618del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406814.1:c.2703_2706del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406815.1:c.2703_2706del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406816.1:c.2703_2706del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406817.1:c.2043_2046del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406818.1:c.3312_3315del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406819.1:c.3312_3315del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406820.1:c.3312_3315del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406821.1:c.3312_3315del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406822.1:c.3312_3315del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406823.1:c.2703_2706del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406824.1:c.3312_3315del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406825.1:c.3312_3315del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406826.1:c.3441_3444del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406827.1:c.3312_3315del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406828.1:c.3312_3315del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406829.1:c.2703_2706del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406830.1:c.3312_3315del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406831.1:c.390_393del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406832.1:c.456_459del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001407362.1:c.1554_1557del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NR_176256.1:n.2535TGCA[1] - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176257.1:n.3866TGCA[1] - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176258.1:n.3795TGCA[1] - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176259.1:n.3694TGCA[1] - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176261.1:n.3576TGCA[1] - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Hereditary nonpolyposis colorectal neoplasms
Identifiers:
MeSH: D003123; MedGen: C0009405

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003524642Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Sep 1, 2022) 		germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Neurofibromatosis von Recklinghausen type I phenotype and early onset of cancers in siblings compound heterozygous for mutations in MSH6.

Ostergaard JR, Sunde L, Okkels H.

Am J Med Genet A. 2005 Dec 1;139A(2):96-105; discussion 96.

PubMed [citation]
PMID:
16283678

MSH6 mutations are frequent in hereditary nonpolyposis colorectal cancer families with normal pMSH6 expression as detected by immunohistochemistry.

Okkels H, Lindorff-Larsen K, Thorlasius-Ussing O, Vyberg M, Lindebjerg J, Sunde L, Bernstein I, Klarskov L, Holck S, Krarup HB.

Appl Immunohistochem Mol Morphol. 2012 Oct;20(5):470-7. doi: 10.1097/PAI.0b013e318249739b.

PubMed [citation]
PMID:
22495361
See all PubMed Citations (5)

Details of each submission

From Invitae, SCV003524642.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

For these reasons, this variant has been classified as Pathogenic. This variant is also known as c.3607_3610delCATG or c.3603_3606delAGTG. This premature translational stop signal has been observed in individual(s) with MSH6-related conditions (PMID: 16283678, 22495361). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.His1203Glnfs*12) in the MSH6 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in MSH6 are known to be pathogenic (PMID: 18269114, 24362816).

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

Last Updated: Jun 17, 2024