NM_000179.3(MSH6):c.884_960del (p.Lys295fs) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Dec 16, 2022
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:: RCV003477319.1

Allele description [Variation Report for NM_000179.3(MSH6):c.884_960del (p.Lys295fs)]

NM_000179.3(MSH6):c.884_960del (p.Lys295fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

2p16.3

Genomic location:

Preferred name:

NM_000179.3(MSH6):c.884_960del (p.Lys295fs)

HGVS:

NC_000002.12:g.47798867_47798943del
NG_007111.1:g.20721_20797del
NM_000179.3:c.884_960delMANE SELECT
NM_001281492.2:c.494_570del
NM_001281493.2:c.-23_54del
NM_001281494.2:c.-23_54del
NM_001406795.1:c.980_1056del
NM_001406796.1:c.884_960del
NM_001406797.1:c.587_663del
NM_001406798.1:c.884_960del
NM_001406799.1:c.359_435del
NM_001406800.1:c.884_960del
NM_001406801.1:c.587_663del
NM_001406802.1:c.980_1056del
NM_001406803.1:c.884_960del
NM_001406804.1:c.806_882del
NM_001406805.1:c.587_663del
NM_001406806.1:c.359_435del
NM_001406807.1:c.359_435del
NM_001406808.1:c.884_960del
NM_001406809.1:c.884_960del
NM_001406811.1:c.-23_54del
NM_001406812.1:c.-23_54del
NM_001406813.1:c.890_966del
NM_001406814.1:c.-23_54del
NM_001406815.1:c.-23_54del
NM_001406816.1:c.-23_54del
NM_001406817.1:c.884_960del
NM_001406818.1:c.587_663del
NM_001406819.1:c.587_663del
NM_001406820.1:c.587_663del
NM_001406821.1:c.587_663del
NM_001406822.1:c.587_663del
NM_001406823.1:c.-23_54del
NM_001406824.1:c.587_663del
NM_001406825.1:c.587_663del
NM_001406826.1:c.716_792del
NM_001406827.1:c.587_663del
NM_001406828.1:c.587_663del
NM_001406829.1:c.-23_54del
NM_001406830.1:c.587_663del
NM_001407362.1:c.628-1799_628-1723del
NP_000170.1:p.Lys295Ilefs
NP_000170.1:p.Lys295fs
NP_001268421.1:p.Lys165fs
NP_001268422.1:p.Met1fs
NP_001268423.1:p.Met1fs
NP_001393724.1:p.Lys327fs
NP_001393725.1:p.Lys295fs
NP_001393726.1:p.Lys196fs
NP_001393727.1:p.Lys295fs
NP_001393728.1:p.Lys120fs
NP_001393729.1:p.Lys295fs
NP_001393730.1:p.Lys196fs
NP_001393731.1:p.Lys327fs
NP_001393732.1:p.Lys295fs
NP_001393733.1:p.Lys269fs
NP_001393734.1:p.Lys196fs
NP_001393735.1:p.Lys120fs
NP_001393736.1:p.Lys120fs
NP_001393737.1:p.Lys295fs
NP_001393738.1:p.Lys295fs
NP_001393740.1:p.Met1fs
NP_001393741.1:p.Met1fs
NP_001393742.1:p.Lys297fs
NP_001393743.1:p.Met1fs
NP_001393744.1:p.Met1fs
NP_001393745.1:p.Met1fs
NP_001393746.1:p.Lys295fs
NP_001393747.1:p.Lys196fs
NP_001393748.1:p.Lys196fs
NP_001393749.1:p.Lys196fs
NP_001393750.1:p.Lys196fs
NP_001393751.1:p.Lys196fs
NP_001393752.1:p.Met1fs
NP_001393753.1:p.Lys196fs
NP_001393754.1:p.Lys196fs
NP_001393755.1:p.Lys239fs
NP_001393756.1:p.Lys196fs
NP_001393757.1:p.Lys196fs
NP_001393758.1:p.Met1fs
NP_001393759.1:p.Lys196fs
LRG_219t1:c.884_960del
LRG_219:g.20721_20797del
NC_000002.11:g.48026006_48026082del
NM_000179.2:c.884_960del
NM_000179.2:c.884_960del77
NR_176257.1:n.973_1049del
NR_176258.1:n.973_1049del
NR_176259.1:n.973_1049del
NR_176261.1:n.973_1049del

Protein change:

K120fs

Molecular consequence:

NM_000179.3:c.884_960del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001281492.2:c.494_570del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001281493.2:c.-23_54del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001281494.2:c.-23_54del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406795.1:c.980_1056del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406796.1:c.884_960del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406797.1:c.587_663del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406798.1:c.884_960del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406799.1:c.359_435del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406800.1:c.884_960del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406801.1:c.587_663del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406802.1:c.980_1056del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406803.1:c.884_960del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406804.1:c.806_882del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406805.1:c.587_663del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406806.1:c.359_435del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406807.1:c.359_435del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406808.1:c.884_960del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406809.1:c.884_960del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406811.1:c.-23_54del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406812.1:c.-23_54del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406813.1:c.890_966del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406814.1:c.-23_54del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406815.1:c.-23_54del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406816.1:c.-23_54del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406817.1:c.884_960del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406818.1:c.587_663del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406819.1:c.587_663del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406820.1:c.587_663del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406821.1:c.587_663del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406822.1:c.587_663del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406823.1:c.-23_54del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406824.1:c.587_663del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406825.1:c.587_663del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406826.1:c.716_792del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406827.1:c.587_663del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406828.1:c.587_663del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406829.1:c.-23_54del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406830.1:c.587_663del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001281493.2:c.-23_54del - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001281494.2:c.-23_54del - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001406811.1:c.-23_54del - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001406812.1:c.-23_54del - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001406814.1:c.-23_54del - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001406815.1:c.-23_54del - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001406816.1:c.-23_54del - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001406823.1:c.-23_54del - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001406829.1:c.-23_54del - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001407362.1:c.628-1799_628-1723del - intron variant - [Sequence Ontology: SO:0001627]
NR_176257.1:n.973_1049del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176258.1:n.973_1049del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176259.1:n.973_1049del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176261.1:n.973_1049del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Ochthebius lividipennis 18S ribosomal RNA gene, partial sequence
Ochthebius lividipennis 18S ribosomal RNA gene, partial sequence
gi|969531091|gb|KT199113.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004222062	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Likely pathogenic (Dec 16, 2022)	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

SCV004222062

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(Quest Diagnostics criteria)

Likely pathogenic
(Dec 16, 2022)

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, SCV004222062.1

#	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. The variant has not been reported in individuals with MSH6-related diseases in the published literature. It also has not been reported in large, multi-ethnic general populations (http://gnomad.broadinstitute.org). Based on the available information, this variant is classified as 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: Jan 6, 2024

ClinVar

Relating variation to medicine