NM_000179.3(MSH6):c.4002-19_4002-10del AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 1, 2023
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:: RCV003477317.1

Allele description [Variation Report for NM_000179.3(MSH6):c.4002-19_4002-10del]

NM_000179.3(MSH6):c.4002-19_4002-10del

Gene:

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

Variant type:

Deletion

Cytogenetic location:

2p16.3

Genomic location:

Preferred name:

NM_000179.3(MSH6):c.4002-19_4002-10del

HGVS:

NC_000002.12:g.47806760_47806769del
NG_007111.1:g.28614_28623del
NG_008397.1:g.103915_103924del
NM_000179.3:c.4002-19_4002-10delMANE SELECT
NM_001281492.2:c.3612-19_3612-10del
NM_001281493.2:c.3096-19_3096-10del
NM_001281494.2:c.3096-19_3096-10del
NM_001406795.1:c.4098-19_4098-10del
NM_001406796.1:c.4002-19_4002-10del
NM_001406797.1:c.3705-19_3705-10del
NM_001406798.1:c.3828-19_3828-10del
NM_001406799.1:c.3477-19_3477-10del
NM_001406800.1:c.*23-19_*23-10del
NM_001406801.1:c.3705-24_3705-15del
NM_001406802.1:c.3898-19_3898-10del
NM_001406803.1:c.3138-19_3138-10del
NM_001406804.1:c.3924-19_3924-10del
NM_001406805.1:c.3705-19_3705-10del
NM_001406806.1:c.3477-19_3477-10del
NM_001406807.1:c.3477-19_3477-10del
NM_001406808.1:c.4002-24_4002-15del
NM_001406809.1:c.4002-19_4002-10del
NM_001406811.1:c.3096-19_3096-10del
NM_001406812.1:c.3096-19_3096-10del
NM_001406813.1:c.4008-19_4008-10del
NM_001406814.1:c.3096-19_3096-10del
NM_001406815.1:c.3096-19_3096-10del
NM_001406816.1:c.3096-19_3096-10del
NM_001406817.1:c.2436-19_2436-10del
NM_001406818.1:c.3705-19_3705-10del
NM_001406819.1:c.3705-19_3705-10del
NM_001406820.1:c.3705-19_3705-10del
NM_001406821.1:c.3705-19_3705-10del
NM_001406822.1:c.3705-24_3705-15del
NM_001406823.1:c.3096-19_3096-10del
NM_001406824.1:c.3705-19_3705-10del
NM_001406825.1:c.3705-19_3705-10del
NM_001406826.1:c.3834-19_3834-10del
NM_001406827.1:c.3705-19_3705-10del
NM_001406828.1:c.3705-19_3705-10del
NM_001406829.1:c.3096-19_3096-10del
NM_001406830.1:c.3705-19_3705-10del
NM_001406831.1:c.783-19_783-10del
NM_001406832.1:c.849-19_849-10del
NM_001407362.1:c.1947-19_1947-10del
LRG_219t1:c.4002-19_4002-10del
LRG_219:g.28614_28623del
NC_000002.11:g.48033899_48033908del
NM_000179.2:c.4002-19_4002-10del

Molecular consequence:

NM_000179.3:c.4002-19_4002-10del - intron variant - [Sequence Ontology: SO:0001627]
NM_001281492.2:c.3612-19_3612-10del - intron variant - [Sequence Ontology: SO:0001627]
NM_001281493.2:c.3096-19_3096-10del - intron variant - [Sequence Ontology: SO:0001627]
NM_001281494.2:c.3096-19_3096-10del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406795.1:c.4098-19_4098-10del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406796.1:c.4002-19_4002-10del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406797.1:c.3705-19_3705-10del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406798.1:c.3828-19_3828-10del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406799.1:c.3477-19_3477-10del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406800.1:c.*23-19_*23-10del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406801.1:c.3705-24_3705-15del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406802.1:c.3898-19_3898-10del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406803.1:c.3138-19_3138-10del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406804.1:c.3924-19_3924-10del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406805.1:c.3705-19_3705-10del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406806.1:c.3477-19_3477-10del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406807.1:c.3477-19_3477-10del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406808.1:c.4002-24_4002-15del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406809.1:c.4002-19_4002-10del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406811.1:c.3096-19_3096-10del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406812.1:c.3096-19_3096-10del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406813.1:c.4008-19_4008-10del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406814.1:c.3096-19_3096-10del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406815.1:c.3096-19_3096-10del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406816.1:c.3096-19_3096-10del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406817.1:c.2436-19_2436-10del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406818.1:c.3705-19_3705-10del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406819.1:c.3705-19_3705-10del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406820.1:c.3705-19_3705-10del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406821.1:c.3705-19_3705-10del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406822.1:c.3705-24_3705-15del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406823.1:c.3096-19_3096-10del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406824.1:c.3705-19_3705-10del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406825.1:c.3705-19_3705-10del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406826.1:c.3834-19_3834-10del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406827.1:c.3705-19_3705-10del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406828.1:c.3705-19_3705-10del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406829.1:c.3096-19_3096-10del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406830.1:c.3705-19_3705-10del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406831.1:c.783-19_783-10del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406832.1:c.849-19_849-10del - intron variant - [Sequence Ontology: SO:0001627]
NM_001407362.1:c.1947-19_1947-10del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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PREDICTED: Homo sapiens STEAP3 metalloreductase (STEAP3), transcript variant X1,...
PREDICTED: Homo sapiens STEAP3 metalloreductase (STEAP3), transcript variant X1, mRNA
gi|767918678|ref|XM_011511403.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004222034	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Uncertain significance (Jun 1, 2023)	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

SCV004222034

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(Quest Diagnostics criteria)

Uncertain significance
(Jun 1, 2023)

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, SCV004222034.1

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

Description

To the best of our knowledge, this variant has not been reported in the published literature. It also has not been reported in large, multi-ethnic general populations (Genome Aggregation Database, http://gnomad.broadinstitute.org). Analysis of this variant using software algorithms for the prediction of the effect of nucleotide changes on splicing yielded predictions that this variant may affect proper MSH6 mRNA splicing . Based on the available information, we are unable to determine the clinical significance of this variant.

#	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

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