NM_000179.3(MSH6):c.3817_3822del (p.Asn1273_Glu1274del) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 17, 2016
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:: RCV000565085.3

Allele description [Variation Report for NM_000179.3(MSH6):c.3817_3822del (p.Asn1273_Glu1274del)]

NM_000179.3(MSH6):c.3817_3822del (p.Asn1273_Glu1274del)

Gene:

MSH6:mutS homolog 6 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

2p16.3

Genomic location:

Preferred name:

NM_000179.3(MSH6):c.3817_3822del (p.Asn1273_Glu1274del)

HGVS:

NC_000002.12:g.47806467_47806472del
NG_007111.1:g.28321_28326del
NG_008397.1:g.104207_104212del
NM_000179.3:c.3817_3822delMANE SELECT
NM_001281492.2:c.3427_3432del
NM_001281493.2:c.2911_2916del
NM_001281494.2:c.2911_2916del
NP_000170.1:p.Asn1273_Glu1274del
NP_001268421.1:p.Asn1143_Glu1144del
NP_001268422.1:p.Asn971_Glu972del
NP_001268423.1:p.Asn971_Glu972del
LRG_219:g.28321_28326del
NC_000002.11:g.48033606_48033611del
NM_000179.2:c.3817_3822delAATGAA

Links:

dbSNP: rs1553333314

NCBI 1000 Genomes Browser:

rs1553333314

Molecular consequence:

NM_000179.3:c.3817_3822del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001281492.2:c.3427_3432del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001281493.2:c.2911_2916del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001281494.2:c.2911_2916del - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000662454	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Mar 17, 2016)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000662454

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Mar 17, 2016)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Ambry Genetics, SCV000662454.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The c.3817_3822delAATGAA variant (also known as p.N1273_E1274del) is located in coding exon 9 of the MSH6 gene. This variant results from an in-frame deletion of 6 nucleotides at positions 3817 to 3822, causing the removal of 2 highly-conserved amino acids at codons 1273 and 1274. This variant was not reported in population based cohorts in the following databases: Database of Single Nucleotide Polymorphisms (dbSNP), NHLBI Exome Sequencing Project (ESP), and 1000 Genomes Project. In the ESP, this variant was not observed in 6503 samples (13006 alleles) with coverage at this position. To date, this alteration has been detected with an allele frequency of approximately 0.001% (greater than 115000 alleles tested) in our clinical cohort. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: May 1, 2024

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