NM_000179.3(MSH6):c.3513_3528del (p.Arg1172fs) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jul 2, 2021
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:: RCV002481103.1

Allele description [Variation Report for NM_000179.3(MSH6):c.3513_3528del (p.Arg1172fs)]

NM_000179.3(MSH6):c.3513_3528del (p.Arg1172fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

2p16.3

Genomic location:

Preferred name:

NM_000179.3(MSH6):c.3513_3528del (p.Arg1172fs)

HGVS:

NC_000002.12:g.47804984_47804999del
NG_007111.1:g.26838_26853del
NG_008397.1:g.105679_105694del
NM_000179.3:c.3513_3528delMANE SELECT
NM_001281492.2:c.3123_3138del
NM_001281493.2:c.2607_2622del
NM_001281494.2:c.2607_2622del
NM_001406795.1:c.3609_3624del16
NM_001406796.1:c.3513_3528del16
NM_001406797.1:c.3216_3231del16
NM_001406798.1:c.3339_3354del16
NM_001406799.1:c.2988_3003del16
NM_001406800.1:c.3513_3528del16
NM_001406801.1:c.3216_3231del16
NM_001406802.1:c.3609_3624del16
NM_001406803.1:c.2649_2664del16
NM_001406804.1:c.3435_3450del16
NM_001406805.1:c.3216_3231del16
NM_001406806.1:c.2988_3003del16
NM_001406807.1:c.2988_3003del16
NM_001406808.1:c.3513_3528del16
NM_001406809.1:c.3513_3528del16
NM_001406811.1:c.2607_2622del16
NM_001406812.1:c.2607_2622del16
NM_001406813.1:c.3519_3534del16
NM_001406814.1:c.2607_2622del16
NM_001406815.1:c.2607_2622del16
NM_001406816.1:c.2607_2622del16
NM_001406817.1:c.1947_1962del16
NM_001406818.1:c.3216_3231del16
NM_001406819.1:c.3216_3231del16
NM_001406820.1:c.3216_3231del16
NM_001406821.1:c.3216_3231del16
NM_001406822.1:c.3216_3231del16
NM_001406823.1:c.2607_2622del16
NM_001406824.1:c.3216_3231del16
NM_001406825.1:c.3216_3231del16
NM_001406826.1:c.3345_3360del16
NM_001406827.1:c.3216_3231del16
NM_001406828.1:c.3216_3231del16
NM_001406829.1:c.2607_2622del16
NM_001406830.1:c.3216_3231del16
NM_001406831.1:c.294_309del16
NM_001406832.1:c.360_375del16
NM_001407362.1:c.1458_1473del16
NP_000170.1:p.Arg1172Leufs
NP_000170.1:p.Arg1172fs
NP_001268421.1:p.Arg1042fs
NP_001268422.1:p.Arg870fs
NP_001268423.1:p.Arg870fs
NP_001393724.1:p.Arg1204Leufs
NP_001393725.1:p.Arg1172Leufs
NP_001393726.1:p.Arg1073Leufs
NP_001393727.1:p.Arg1114Leufs
NP_001393728.1:p.Arg997Leufs
NP_001393729.1:p.Arg1172Leufs
NP_001393730.1:p.Arg1073Leufs
NP_001393731.1:p.Arg1204Leufs
NP_001393732.1:p.Arg884Leufs
NP_001393733.1:p.Arg1146Leufs
NP_001393734.1:p.Arg1073Leufs
NP_001393735.1:p.Arg997Leufs
NP_001393736.1:p.Arg997Leufs
NP_001393737.1:p.Arg1172Leufs
NP_001393738.1:p.Arg1172Leufs
NP_001393740.1:p.Arg870Leufs
NP_001393741.1:p.Arg870Leufs
NP_001393742.1:p.Arg1174Leufs
NP_001393743.1:p.Arg870Leufs
NP_001393744.1:p.Arg870Leufs
NP_001393745.1:p.Arg870Leufs
NP_001393746.1:p.Arg650Leufs
NP_001393747.1:p.Arg1073Leufs
NP_001393748.1:p.Arg1073Leufs
NP_001393749.1:p.Arg1073Leufs
NP_001393750.1:p.Arg1073Leufs
NP_001393751.1:p.Arg1073Leufs
NP_001393752.1:p.Arg870Leufs
NP_001393753.1:p.Arg1073Leufs
NP_001393754.1:p.Arg1073Leufs
NP_001393755.1:p.Arg1116Leufs
NP_001393756.1:p.Arg1073Leufs
NP_001393757.1:p.Arg1073Leufs
NP_001393758.1:p.Arg870Leufs
NP_001393759.1:p.Arg1073Leufs
NP_001393760.1:p.Arg99Leufs
NP_001393761.1:p.Arg121Leufs
NP_001394291.1:p.Arg487Leufs
LRG_219t1:c.3513_3528del
LRG_219:g.26838_26853del
NC_000002.11:g.48032123_48032138del
NM_000179.2:c.3513_3528del
NM_000179.2:c.3513_3528del16
NR_176256.1:n.2443_2458del16
NR_176257.1:n.3774_3789del16
NR_176258.1:n.3703_3718del16
NR_176259.1:n.3602_3617del16
NR_176260.1:n.1547_1562del16

Protein change:

R1042fs

Molecular consequence:

NM_000179.3:c.3513_3528del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001281492.2:c.3123_3138del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001281493.2:c.2607_2622del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001281494.2:c.2607_2622del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406795.1:c.3609_3624del16 - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406796.1:c.3513_3528del16 - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406797.1:c.3216_3231del16 - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406798.1:c.3339_3354del16 - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406799.1:c.2988_3003del16 - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406800.1:c.3513_3528del16 - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406801.1:c.3216_3231del16 - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406802.1:c.3609_3624del16 - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406803.1:c.2649_2664del16 - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406804.1:c.3435_3450del16 - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406805.1:c.3216_3231del16 - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406806.1:c.2988_3003del16 - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406807.1:c.2988_3003del16 - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406808.1:c.3513_3528del16 - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406809.1:c.3513_3528del16 - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406811.1:c.2607_2622del16 - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406812.1:c.2607_2622del16 - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406813.1:c.3519_3534del16 - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406814.1:c.2607_2622del16 - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406815.1:c.2607_2622del16 - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406816.1:c.2607_2622del16 - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406817.1:c.1947_1962del16 - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406818.1:c.3216_3231del16 - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406819.1:c.3216_3231del16 - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406820.1:c.3216_3231del16 - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406821.1:c.3216_3231del16 - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406822.1:c.3216_3231del16 - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406823.1:c.2607_2622del16 - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406824.1:c.3216_3231del16 - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406825.1:c.3216_3231del16 - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406826.1:c.3345_3360del16 - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406827.1:c.3216_3231del16 - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406828.1:c.3216_3231del16 - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406829.1:c.2607_2622del16 - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406830.1:c.3216_3231del16 - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406831.1:c.294_309del16 - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406832.1:c.360_375del16 - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407362.1:c.1458_1473del16 - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Arabidopsis thaliana other RNA (AT5G05435), lncRNA
Arabidopsis thaliana other RNA (AT5G05435), lncRNA
gi|1063743973|ref|NR_142834.1|

Nucleotide
Klebsiella variicola strain CH4 contig1, whole genome shotgun sequence
Klebsiella variicola strain CH4 contig1, whole genome shotgun sequence
gi|821223988|gb|JSXA01000001.1||gnl JSXA01|contig1

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002774283	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Likely pathogenic (Jul 2, 2021)	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

SCV002774283

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(Quest Diagnostics criteria)

Likely pathogenic
(Jul 2, 2021)

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	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 Quest Diagnostics Nichols Institute San Juan Capistrano, SCV002774283.1

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

Description

This frameshift variant alters the translational reading frame of the MSH6 mRNA and is predicted to cause the premature termination of MSH6 protein synthesis. To the best of our knowledge, the variant has not been reported in the published literature. Based on the available information, the variant is predicted to be likely pathogenic.

#	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: Mar 26, 2023

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Relating variation to medicine