NM_000179.3(MSH6):c.1938G>A (p.Lys646=) AND not provided

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Jul 23, 2020
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:: RCV000827019.6

Allele description [Variation Report for NM_000179.3(MSH6):c.1938G>A (p.Lys646=)]

NM_000179.3(MSH6):c.1938G>A (p.Lys646=)

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.1938G>A (p.Lys646=)

HGVS:

NC_000002.12:g.47799921G>A
NG_007111.1:g.21775G>A
NM_000179.3:c.1938G>AMANE SELECT
NM_001281492.2:c.1548G>A
NM_001281493.2:c.1032G>A
NM_001281494.2:c.1032G>A
NP_000170.1:p.Lys646=
NP_000170.1:p.Lys646=
NP_001268421.1:p.Lys516=
NP_001268422.1:p.Lys344=
NP_001268423.1:p.Lys344=
LRG_219t1:c.1938G>A
LRG_219:g.21775G>A
LRG_219p1:p.Lys646=
NC_000002.11:g.48027060G>A
NM_000179.2:c.1938G>A

Links:

dbSNP: rs758631207

NCBI 1000 Genomes Browser:

rs758631207

Molecular consequence:

NM_000179.3:c.1938G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001281492.2:c.1548G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001281493.2:c.1032G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001281494.2:c.1032G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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gi|393186579|gb|JX083927.1|

Nucleotide
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BioProject
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long-wavelength rhodopsin, partial [Osmia rhodoensis]
gi|194441988|gb|ACF71369.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000968630	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Likely benign (May 4, 2018)	germline	clinical testing	Citation Link,
SCV001469821	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Likely benign (Jul 23, 2020)	unknown	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

SCV000968630

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Likely benign
(May 4, 2018)

germline

clinical testing

Citation Link,

SCV001469821

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(Quest Diagnostics criteria)

Likely benign
(Jul 23, 2020)

unknown

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
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]

PMID:: 26467025
PMCID:: PMC4737317

Details of each submission

From GeneDx, SCV000968630.1

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

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

#	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 Quest Diagnostics Nichols Institute San Juan Capistrano, SCV001469821.1

#	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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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