NM_000249.4(MLH1):c.1217G>A (p.Ser406Asn) AND Lynch syndrome

Germline classification:: Benign (2 submissions)
Last evaluated:: Sep 5, 2013
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:: RCV000075152.16

Allele description [Variation Report for NM_000249.4(MLH1):c.1217G>A (p.Ser406Asn)]

NM_000249.4(MLH1):c.1217G>A (p.Ser406Asn)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

3p22.2

Genomic location:

Preferred name:

NM_000249.4(MLH1):c.1217G>A (p.Ser406Asn)

Other names:

p.S406N:AGT>AAT

HGVS:

NC_000003.12:g.37025815G>A
NG_007109.2:g.37466G>A
NM_000249.4:c.1217G>AMANE SELECT
NM_001167617.3:c.923G>A
NM_001167618.3:c.494G>A
NM_001167619.3:c.494G>A
NM_001258271.2:c.1217G>A
NM_001258273.2:c.494G>A
NM_001258274.3:c.494G>A
NM_001354615.2:c.494G>A
NM_001354616.2:c.494G>A
NM_001354617.2:c.494G>A
NM_001354618.2:c.494G>A
NM_001354619.2:c.494G>A
NM_001354620.2:c.923G>A
NM_001354621.2:c.194G>A
NM_001354622.2:c.194G>A
NM_001354623.2:c.194G>A
NM_001354624.2:c.143G>A
NM_001354625.2:c.143G>A
NM_001354626.2:c.143G>A
NM_001354627.2:c.143G>A
NM_001354628.2:c.1217G>A
NM_001354629.2:c.1118G>A
NM_001354630.2:c.1217G>A
NP_000240.1:p.Ser406Asn
NP_000240.1:p.Ser406Asn
NP_001161089.1:p.Ser308Asn
NP_001161090.1:p.Ser165Asn
NP_001161091.1:p.Ser165Asn
NP_001245200.1:p.Ser406Asn
NP_001245202.1:p.Ser165Asn
NP_001245203.1:p.Ser165Asn
NP_001341544.1:p.Ser165Asn
NP_001341545.1:p.Ser165Asn
NP_001341546.1:p.Ser165Asn
NP_001341547.1:p.Ser165Asn
NP_001341548.1:p.Ser165Asn
NP_001341549.1:p.Ser308Asn
NP_001341550.1:p.Ser65Asn
NP_001341551.1:p.Ser65Asn
NP_001341552.1:p.Ser65Asn
NP_001341553.1:p.Ser48Asn
NP_001341554.1:p.Ser48Asn
NP_001341555.1:p.Ser48Asn
NP_001341556.1:p.Ser48Asn
NP_001341557.1:p.Ser406Asn
NP_001341558.1:p.Ser373Asn
NP_001341559.1:p.Ser406Asn
LRG_216t1:c.1217G>A
LRG_216:g.37466G>A
LRG_216p1:p.Ser406Asn
NC_000003.11:g.37067306G>A
NM_000249.3:c.1217G>A
P40692:p.Ser406Asn
p.S406N

Protein change:

S165N

Links:

UniProtKB: P40692#VAR_012919; dbSNP: rs41294980

NCBI 1000 Genomes Browser:

rs41294980

Molecular consequence:

NM_000249.4:c.1217G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001167617.3:c.923G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001167618.3:c.494G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001167619.3:c.494G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001258271.2:c.1217G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001258273.2:c.494G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001258274.3:c.494G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354615.2:c.494G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354616.2:c.494G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354617.2:c.494G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354618.2:c.494G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354619.2:c.494G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354620.2:c.923G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354621.2:c.194G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354622.2:c.194G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354623.2:c.194G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354624.2:c.143G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354625.2:c.143G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354626.2:c.143G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354627.2:c.143G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354628.2:c.1217G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354629.2:c.1118G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354630.2:c.1217G>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

238

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
SCV000106144	International Society for Gastrointestinal Hereditary Tumours (InSiGHT)	reviewed by expert panel (Guidelines v1.9)	no known pathogenicity (Sep 5, 2013)	germline	research	Citation Link,
SCV004840975	All of Us Research Program, National Institutes of Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely Benign (Feb 5, 2024)	germline	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

SCV000106144

International Society for Gastrointestinal Hereditary Tumours (InSiGHT)

reviewed by expert panel

(Guidelines v1.9)

no known pathogenicity
(Sep 5, 2013)

germline

research

Citation Link,

SCV004840975

All of Us Research Program, National Institutes of Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely Benign
(Feb 5, 2024)

germline

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	germline	unknown	238	not provided	not provided	108544	not provided	clinical testing, research

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From International Society for Gastrointestinal Hereditary Tumours (InSiGHT), SCV000106144.3

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

Description

Multifactorial likelihood analysis posterior probability <0.001

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From All of Us Research Program, National Institutes of Health, SCV004840975.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	238	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	108544	not provided	not provided		238	not provided	not provided	not provided

Last Updated: Apr 20, 2024

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