NM_000249.4(MLH1):c.293_304del (p.Gly98_Gly101del) AND Lynch syndrome

Germline classification:: Likely pathogenic (1 submission)
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:: RCV000075616.3

Allele description [Variation Report for NM_000249.4(MLH1):c.293_304del (p.Gly98_Gly101del)]

NM_000249.4(MLH1):c.293_304del (p.Gly98_Gly101del)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

3p22.2

Genomic location:

Preferred name:

NM_000249.4(MLH1):c.293_304del (p.Gly98_Gly101del)

HGVS:

NC_000003.12:g.37001040_37001051del
NG_007109.2:g.12691_12702del
NM_000249.4:c.293_304delMANE SELECT
NM_001167617.3:c.4_12+3del
NM_001167618.3:c.-431_-420del
NM_001167619.3:c.-339_-328del
NM_001258271.2:c.293_304del
NM_001258273.2:c.-431_-420del
NM_001258274.3:c.-431_-420del
NM_001354615.2:c.-334_-326+3del
NM_001354616.2:c.-339_-328del
NM_001354617.2:c.-431_-420del
NM_001354618.2:c.-431_-420del
NM_001354619.2:c.-431_-420del
NM_001354620.2:c.4_12+3del
NM_001354621.2:c.-524_-513del
NM_001354622.2:c.-637_-626del
NM_001354623.2:c.-637_-626del
NM_001354624.2:c.-534_-523del
NM_001354625.2:c.-437_-429+3del
NM_001354626.2:c.-534_-523del
NM_001354627.2:c.-534_-523del
NM_001354628.2:c.293_304del
NM_001354629.2:c.208-3361_208-3350del
NM_001354630.2:c.293_304del
NP_000240.1:p.Gly98_Gly101del
NP_000240.1:p.Gly98_Gly101del
NP_001245200.1:p.Gly98_Gly101del
NP_001341557.1:p.Gly98_Gly101del
NP_001341559.1:p.Gly98_Gly101del
LRG_216t1:c.293_304del
LRG_216:g.12691_12702del
LRG_216p1:p.Gly98_Gly101del
NC_000003.11:g.37042531_37042542del
NM_000249.3:c.293_304del

Links:

dbSNP: rs63751691

NCBI 1000 Genomes Browser:

rs63751691

Molecular consequence:

NM_001167618.3:c.-431_-420del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001167619.3:c.-339_-328del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001258273.2:c.-431_-420del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001258274.3:c.-431_-420del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354616.2:c.-339_-328del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354617.2:c.-431_-420del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354618.2:c.-431_-420del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354619.2:c.-431_-420del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354621.2:c.-524_-513del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354622.2:c.-637_-626del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354623.2:c.-637_-626del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354624.2:c.-534_-523del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354626.2:c.-534_-523del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354627.2:c.-534_-523del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000249.4:c.293_304del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001258271.2:c.293_304del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354628.2:c.293_304del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354630.2:c.293_304del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001167617.3:c.4_12+3del - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001354620.2:c.4_12+3del - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001354629.2:c.208-3361_208-3350del - intron variant - [Sequence Ontology: SO:0001627]
NM_001167617.3:c.4_12+3del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001354615.2:c.-334_-326+3del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001354620.2:c.4_12+3del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001354625.2:c.-437_-429+3del - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

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

Recent activity

Clear Turn Off Turn On

LOC101500102 [Cicer arietinum]
LOC101500102 [Cicer arietinum]
Gene ID:101500102

Gene

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000106617	International Society for Gastrointestinal Hereditary Tumours (InSiGHT)	reviewed by expert panel (Guidelines v2.4)	Likely pathogenic (Jun 21, 2019)	germline	curation	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000106617

International Society for Gastrointestinal Hereditary Tumours (InSiGHT)

reviewed by expert panel

(Guidelines v2.4)

Likely pathogenic
(Jun 21, 2019)

germline

curation

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
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), SCV000106617.4

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

Description

Multifactorial likelihood analysis posterior probability 0.95-0.99

#	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

Last Updated: Sep 3, 2023

ClinVar

Relating variation to medicine