NM_000179.3(MSH6):c.38A>G (p.Lys13Arg) AND Hereditary cancer-predisposing syndrome

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Jan 9, 2023
Review status:: criteria provided, conflicting classifications

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:: RCV000771457.6

Allele description [Variation Report for NM_000179.3(MSH6):c.38A>G (p.Lys13Arg)]

NM_000179.3(MSH6):c.38A>G (p.Lys13Arg)

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.38A>G (p.Lys13Arg)

HGVS:

NC_000002.12:g.47783271A>G
NG_007111.1:g.5125A>G
NM_000179.3:c.38A>GMANE SELECT
NM_001281492.2:c.38A>G
NM_001281493.2:c.-699A>G
NP_000170.1:p.Lys13Arg
NP_000170.1:p.Lys13Arg
NP_001268421.1:p.Lys13Arg
LRG_219t1:c.38A>G
LRG_219:g.5125A>G
LRG_219p1:p.Lys13Arg
NC_000002.11:g.48010410A>G
NM_000179.2:c.38A>G

Protein change:

K13R

Links:

dbSNP: rs41294988

NCBI 1000 Genomes Browser:

rs41294988

Molecular consequence:

NM_001281493.2:c.-699A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000179.3:c.38A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001281492.2:c.38A>G - missense variant - [Sequence Ontology: SO:0001583]

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

Recent activity

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far upstream element-binding protein 2 isoform 3 [Homo sapiens]
far upstream element-binding protein 2 isoform 3 [Homo sapiens]
gi|1483569468|ref|NP_001353229.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000903874	Color Diagnostics, LLC DBA Color Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Apr 22, 2016)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002624393	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Jan 9, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000903874

Color Diagnostics, LLC DBA Color Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(Apr 22, 2016)

germline

clinical testing

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

SCV002624393

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Jan 9, 2023)

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Color Diagnostics, LLC DBA Color Health, SCV000903874.1

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

#	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

From Ambry Genetics, SCV002624393.3

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

Description

The p.K13R variant (also known as c.38A>G), located in coding exon 1 of the MSH6 gene, results from an A to G substitution at nucleotide position 38. The lysine at codon 13 is replaced by arginine, an amino acid with highly similar properties. This amino acid position is highly conserved on limited sequence alignment. In addition, the in silico prediction for this alteration is inconclusive. 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: Sep 29, 2024

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