NM_000249.4(MLH1):c.2262del (p.Arg755fs) AND Lynch syndrome

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Jun 21, 2019
Review status:: 3 stars out of maximum of 4 stars
reviewed by expert panel

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:: RCV000075590.12

Allele description [Variation Report for NM_000249.4(MLH1):c.2262del (p.Arg755fs)]

NM_000249.4(MLH1):c.2262del (p.Arg755fs)

Gene:

MLH1:mutL homolog 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

3p22.2

Genomic location:

Preferred name:

NM_000249.4(MLH1):c.2262del (p.Arg755fs)

HGVS:

NC_000003.12:g.37050644del
NG_007109.2:g.62295del
NG_053016.1:g.131174del
NM_000249.4:c.2262delMANE SELECT
NM_001167617.3:c.1968del
NM_001167618.3:c.1539del
NM_001167619.3:c.1539del
NM_001258271.2:c.2055del
NM_001258273.2:c.1539del
NM_001258274.3:c.1539del
NM_001354615.2:c.1539del
NM_001354616.2:c.1539del
NM_001354617.2:c.1539del
NM_001354618.2:c.1539del
NM_001354619.2:c.1539del
NM_001354620.2:c.1968del
NM_001354621.2:c.1239del
NM_001354622.2:c.1239del
NM_001354623.2:c.1239del
NM_001354624.2:c.1188del
NM_001354625.2:c.1188del
NM_001354626.2:c.1188del
NM_001354627.2:c.1188del
NM_001354628.2:c.2169del
NM_001354629.2:c.2163del
NM_001354630.2:c.2097del
NP_000240.1:p.Arg755fs
NP_000240.1:p.Arg755fs
NP_001161089.1:p.Arg657fs
NP_001161090.1:p.Arg514fs
NP_001161091.1:p.Arg514fs
NP_001245200.1:p.Arg686fs
NP_001245202.1:p.Arg514fs
NP_001245203.1:p.Arg514fs
NP_001341544.1:p.Arg514fs
NP_001341545.1:p.Arg514fs
NP_001341546.1:p.Arg514fs
NP_001341547.1:p.Arg514fs
NP_001341548.1:p.Arg514fs
NP_001341549.1:p.Arg657fs
NP_001341550.1:p.Arg414fs
NP_001341551.1:p.Arg414fs
NP_001341552.1:p.Arg414fs
NP_001341553.1:p.Arg397fs
NP_001341554.1:p.Arg397fs
NP_001341555.1:p.Arg397fs
NP_001341556.1:p.Arg397fs
NP_001341557.1:p.Arg724fs
NP_001341558.1:p.Arg722fs
NP_001341559.1:p.Arg700fs
LRG_216t1:c.2262del
LRG_216:g.62295del
LRG_216p1:p.Arg755fs
NC_000003.11:g.37092135del
NC_000003.11:g.37092135delG
NM_000249.3:c.2262del

Protein change:

R397fs

Links:

dbSNP: rs267607904

NCBI 1000 Genomes Browser:

rs267607904

Molecular consequence:

NM_000249.4:c.2262del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001167617.3:c.1968del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001167618.3:c.1539del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001167619.3:c.1539del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001258271.2:c.2055del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001258273.2:c.1539del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001258274.3:c.1539del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354615.2:c.1539del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354616.2:c.1539del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354617.2:c.1539del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354618.2:c.1539del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354619.2:c.1539del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354620.2:c.1968del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354621.2:c.1239del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354622.2:c.1239del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354623.2:c.1239del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354624.2:c.1188del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354625.2:c.1188del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354626.2:c.1188del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354627.2:c.1188del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354628.2:c.2169del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354629.2:c.2163del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354630.2:c.2097del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Lynch syndrome
Identifiers:: MONDO: MONDO:0005835; MedGen: C4552100

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000106587	International Society for Gastrointestinal Hereditary Tumours (InSiGHT)	reviewed by expert panel (Guidelines v2.4)	Uncertain significance (Jun 21, 2019)	germline	curation	Citation Link,
SCV000838031	Mendelics	criteria provided, single submitter (Mendelics Assertion Criteria 2017)	Likely pathogenic (Jul 2, 2018)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000106587

International Society for Gastrointestinal Hereditary Tumours (InSiGHT)

reviewed by expert panel

(Guidelines v2.4)

Uncertain significance
(Jun 21, 2019)

germline

curation

Citation Link,

SCV000838031

Mendelics

criteria provided, single submitter

(Mendelics Assertion Criteria 2017)

Likely pathogenic
(Jul 2, 2018)

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
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	curation

Details of each submission

From International Society for Gastrointestinal Hereditary Tumours (InSiGHT), SCV000106587.3

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

Description

Insufficient evidence: extends protein by 25 amino acids

#	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 Mendelics, SCV000838031.2

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

#	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 26, 2024

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