NM_000179.3(MSH6):c.3974A>T (p.Lys1325Met) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Oct 24, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000485930.5

Allele description [Variation Report for NM_000179.3(MSH6):c.3974A>T (p.Lys1325Met)]

NM_000179.3(MSH6):c.3974A>T (p.Lys1325Met)

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.3974A>T (p.Lys1325Met)

HGVS:

NC_000002.12:g.47806624A>T
NG_007111.1:g.28478A>T
NG_008397.1:g.104052T>A
NM_000179.3:c.3974A>TMANE SELECT
NM_001281492.2:c.3584A>T
NM_001281493.2:c.3068A>T
NM_001281494.2:c.3068A>T
NP_000170.1:p.Lys1325Met
NP_000170.1:p.Lys1325Met
NP_001268421.1:p.Lys1195Met
NP_001268422.1:p.Lys1023Met
NP_001268423.1:p.Lys1023Met
LRG_219t1:c.3974A>T
LRG_219:g.28478A>T
LRG_219p1:p.Lys1325Met
NC_000002.11:g.48033763A>T
NM_000179.2:c.3974A>T

Protein change:

K1023M

Links:

dbSNP: rs876658189

NCBI 1000 Genomes Browser:

rs876658189

Molecular consequence:

NM_000179.3:c.3974A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001281492.2:c.3584A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001281493.2:c.3068A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001281494.2:c.3068A>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000566508	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Oct 24, 2023)	germline	clinical testing	Citation Link,
SCV005199220	Clinical Genetics Laboratory, Skane University Hospital Lund	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (May 27, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000566508

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Oct 24, 2023)

germline

clinical testing

Citation Link,

SCV005199220

Clinical Genetics Laboratory, Skane University Hospital Lund

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(May 27, 2022)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	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 GeneDx, SCV000566508.7

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

Description

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 12019211, 21120944, 17531815)

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

From Clinical Genetics Laboratory, Skane University Hospital Lund, SCV005199220.1

#	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	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Aug 25, 2024

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Relating variation to medicine