NM_000249.4(MLH1):c.636C>T (p.Thr212=) AND Colorectal cancer, hereditary nonpolyposis, type 2

Germline classification:: Benign/Likely benign (2 submissions)
Last evaluated:: Mar 13, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000410585.11

Allele description [Variation Report for NM_000249.4(MLH1):c.636C>T (p.Thr212=)]

NM_000249.4(MLH1):c.636C>T (p.Thr212=)

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.636C>T (p.Thr212=)

HGVS:

NC_000003.12:g.37012058C>T
NG_007109.2:g.23709C>T
NM_000249.4:c.636C>TMANE SELECT
NM_001167617.3:c.342C>T
NM_001167618.3:c.-88C>T
NM_001167619.3:c.-88C>T
NM_001258271.2:c.636C>T
NM_001258273.2:c.-88C>T
NM_001258274.3:c.-88C>T
NM_001354615.2:c.-88C>T
NM_001354616.2:c.-88C>T
NM_001354617.2:c.-88C>T
NM_001354618.2:c.-88C>T
NM_001354619.2:c.-88C>T
NM_001354620.2:c.342C>T
NM_001354621.2:c.-181C>T
NM_001354622.2:c.-294C>T
NM_001354623.2:c.-294C>T
NM_001354624.2:c.-191C>T
NM_001354625.2:c.-191C>T
NM_001354626.2:c.-191C>T
NM_001354627.2:c.-191C>T
NM_001354628.2:c.636C>T
NM_001354629.2:c.537C>T
NM_001354630.2:c.636C>T
NP_000240.1:p.Thr212=
NP_000240.1:p.Thr212=
NP_001161089.1:p.Thr114=
NP_001245200.1:p.Thr212=
NP_001341549.1:p.Thr114=
NP_001341557.1:p.Thr212=
NP_001341558.1:p.Thr179=
NP_001341559.1:p.Thr212=
LRG_216t1:c.636C>T
LRG_216:g.23709C>T
LRG_216p1:p.Thr212=
NC_000003.11:g.37053549C>T
NM_000249.3:c.636C>T
p.T212T

Links:

dbSNP: rs138735345

NCBI 1000 Genomes Browser:

rs138735345

Molecular consequence:

NM_001167618.3:c.-88C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001167619.3:c.-88C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001258273.2:c.-88C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001258274.3:c.-88C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354615.2:c.-88C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354616.2:c.-88C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354617.2:c.-88C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354618.2:c.-88C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354619.2:c.-88C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354621.2:c.-181C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354622.2:c.-294C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354623.2:c.-294C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354624.2:c.-191C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354625.2:c.-191C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354626.2:c.-191C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001354627.2:c.-191C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000249.4:c.636C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001167617.3:c.342C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001258271.2:c.636C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354620.2:c.342C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354628.2:c.636C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354629.2:c.537C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354630.2:c.636C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:: Colorectal cancer, hereditary nonpolyposis, type 2 (LYNCH2)
Synonyms:: COLON CANCER, FAMILIAL NONPOLYPOSIS, TYPE 2; Lynch syndrome II; MLH1-Related Lynch Syndrome; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0012249; MedGen: C1333991; Orphanet: 144; OMIM: 609310

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000487838	Counsyl	criteria provided, single submitter (Counsyl Autosomal Dominant Disease Classification criteria (2015))	Likely benign (Nov 20, 2015)	unknown	clinical testing	Counsyl Autosomal Dominant Disease Classification criteria (2015), Citation Link,
SCV004018113	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))	Benign (Mar 13, 2023)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000487838

Counsyl

criteria provided, single submitter

(Counsyl Autosomal Dominant Disease Classification criteria (2015))

Likely benign
(Nov 20, 2015)

unknown

clinical testing

Counsyl Autosomal Dominant Disease Classification criteria (2015),

Citation Link,

SCV004018113

Myriad Genetics, Inc.

criteria provided, single submitter

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

Benign
(Mar 13, 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 Counsyl, SCV000487838.2

#	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

From Myriad Genetics, Inc., SCV004018113.1

#	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 benign. This variant is a silent/synonymous amino acid change and it is not expected to impact splicing.

#	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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