NM_000179.3(MSH6):c.3926del (p.Pro1309fs) AND Lynch syndrome 5

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 28, 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:: RCV003450313.1

Allele description [Variation Report for NM_000179.3(MSH6):c.3926del (p.Pro1309fs)]

NM_000179.3(MSH6):c.3926del (p.Pro1309fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

2p16.3

Genomic location:

Preferred name:

NM_000179.3(MSH6):c.3926del (p.Pro1309fs)

HGVS:

NC_000002.12:g.47806576del
NG_007111.1:g.28430del
NG_008397.1:g.104102del
NM_000179.3:c.3926delMANE SELECT
NM_001281492.2:c.3536del
NM_001281493.2:c.3020del
NM_001281494.2:c.3020del
NM_001406795.1:c.4022del
NM_001406796.1:c.3926del
NM_001406797.1:c.3629del
NM_001406798.1:c.3752del
NM_001406799.1:c.3401del
NM_001406800.1:c.3913del
NM_001406801.1:c.3629del
NM_001406802.1:c.3898-203del
NM_001406803.1:c.3062del
NM_001406804.1:c.3848del
NM_001406805.1:c.3629del
NM_001406806.1:c.3401del
NM_001406807.1:c.3401del
NM_001406808.1:c.3926del
NM_001406809.1:c.3926del
NM_001406811.1:c.3020del
NM_001406812.1:c.3020del
NM_001406813.1:c.3932del
NM_001406814.1:c.3020del
NM_001406815.1:c.3020del
NM_001406816.1:c.3020del
NM_001406817.1:c.2360del
NM_001406818.1:c.3629del
NM_001406819.1:c.3629del
NM_001406820.1:c.3629del
NM_001406821.1:c.3629del
NM_001406822.1:c.3629del
NM_001406823.1:c.3020del
NM_001406824.1:c.3629del
NM_001406825.1:c.3629del
NM_001406826.1:c.3758del
NM_001406827.1:c.3629del
NM_001406828.1:c.3629del
NM_001406829.1:c.3020del
NM_001406830.1:c.3629del
NM_001406831.1:c.707del
NM_001406832.1:c.773del
NM_001407362.1:c.1871del
NP_000170.1:p.Pro1309Glnfs
NP_000170.1:p.Pro1309fs
NP_001268421.1:p.Pro1179fs
NP_001268422.1:p.Pro1007fs
NP_001268423.1:p.Pro1007fs
NP_001393724.1:p.Pro1341fs
NP_001393725.1:p.Pro1309fs
NP_001393726.1:p.Pro1210fs
NP_001393727.1:p.Pro1251fs
NP_001393728.1:p.Pro1134fs
NP_001393729.1:p.Gln1305fs
NP_001393730.1:p.Pro1210fs
NP_001393732.1:p.Pro1021fs
NP_001393733.1:p.Pro1283fs
NP_001393734.1:p.Pro1210fs
NP_001393735.1:p.Pro1134fs
NP_001393736.1:p.Pro1134fs
NP_001393737.1:p.Pro1309fs
NP_001393738.1:p.Pro1309fs
NP_001393740.1:p.Pro1007fs
NP_001393741.1:p.Pro1007fs
NP_001393742.1:p.Pro1311fs
NP_001393743.1:p.Pro1007fs
NP_001393744.1:p.Pro1007fs
NP_001393745.1:p.Pro1007fs
NP_001393746.1:p.Pro787fs
NP_001393747.1:p.Pro1210fs
NP_001393748.1:p.Pro1210fs
NP_001393749.1:p.Pro1210fs
NP_001393750.1:p.Pro1210fs
NP_001393751.1:p.Pro1210fs
NP_001393752.1:p.Pro1007fs
NP_001393753.1:p.Pro1210fs
NP_001393754.1:p.Pro1210fs
NP_001393755.1:p.Pro1253fs
NP_001393756.1:p.Pro1210fs
NP_001393757.1:p.Pro1210fs
NP_001393758.1:p.Pro1007fs
NP_001393759.1:p.Pro1210fs
NP_001393760.1:p.Pro236fs
NP_001393761.1:p.Pro258fs
NP_001394291.1:p.Pro624fs
LRG_219t1:c.3926del
LRG_219:g.28430del
LRG_219p1:p.Pro1309Glnfs
NC_000002.11:g.48033715del
NM_000179.2:c.3926delC
NR_176256.1:n.2856del
NR_176257.1:n.4187del
NR_176258.1:n.4116del
NR_176259.1:n.4015del
NR_176260.1:n.1960delC
NR_176261.1:n.3897del

Protein change:

P1007fs

Molecular consequence:

NM_000179.3:c.3926del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001281492.2:c.3536del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001281493.2:c.3020del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001281494.2:c.3020del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406795.1:c.4022del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406796.1:c.3926del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406797.1:c.3629del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406798.1:c.3752del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406799.1:c.3401del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406800.1:c.3913del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406801.1:c.3629del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406803.1:c.3062del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406804.1:c.3848del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406805.1:c.3629del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406806.1:c.3401del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406807.1:c.3401del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406808.1:c.3926del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406809.1:c.3926del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406811.1:c.3020del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406812.1:c.3020del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406813.1:c.3932del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406814.1:c.3020del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406815.1:c.3020del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406816.1:c.3020del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406817.1:c.2360del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406818.1:c.3629del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406819.1:c.3629del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406820.1:c.3629del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406821.1:c.3629del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406822.1:c.3629del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406823.1:c.3020del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406824.1:c.3629del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406825.1:c.3629del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406826.1:c.3758del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406827.1:c.3629del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406828.1:c.3629del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406829.1:c.3020del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406830.1:c.3629del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406831.1:c.707del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406832.1:c.773del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407362.1:c.1871del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406802.1:c.3898-203del - intron variant - [Sequence Ontology: SO:0001627]
NR_176256.1:n.2856del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176257.1:n.4187del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176258.1:n.4116del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176259.1:n.4015del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176261.1:n.3897del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Lynch syndrome 5 (LYNCH5)
Synonyms:: Colorectal cancer, hereditary nonpolyposis, type 5; Hereditary non-polyposis colorectal cancer, type 5
Identifiers:: MONDO: MONDO:0013710; MedGen: C1833477; Orphanet: 144; OMIM: 614350

Recent activity

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Homo sapiens secernin 2 (SCRN2), transcript variant 1, mRNA
Homo sapiens secernin 2 (SCRN2), transcript variant 1, mRNA
gi|1519242558|ref|NM_138355.4|

Nucleotide
Homo sapiens secernin 2, mRNA (cDNA clone MGC:15359 IMAGE:3945715), complete cds
Homo sapiens secernin 2, mRNA (cDNA clone MGC:15359 IMAGE:3945715), complete cds
gi|39645194|gb|BC010408.2|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004187108	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))	Pathogenic (Aug 28, 2023)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004187108

Myriad Genetics, Inc.

criteria provided, single submitter

(Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))

Pathogenic
(Aug 28, 2023)

unknown

clinical testing

Citation Link

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

Details of each submission

From Myriad Genetics, Inc., SCV004187108.1

#	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 pathogenic. This variant creates a frameshift predicted to result in premature protein truncation.

#	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: Oct 8, 2024

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