NM_000249.4(MLH1):c.1732-3T>C AND Hereditary nonpolyposis colorectal neoplasms

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Apr 19, 2022
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:: RCV001341182.3

Allele description [Variation Report for NM_000249.4(MLH1):c.1732-3T>C]

NM_000249.4(MLH1):c.1732-3T>C

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.1732-3T>C

HGVS:

NC_000003.12:g.37047516T>C
NG_007109.2:g.59167T>C
NM_000249.4:c.1732-3T>CMANE SELECT
NM_001167617.3:c.1438-3T>C
NM_001167618.3:c.1009-3T>C
NM_001167619.3:c.1009-3T>C
NM_001258271.2:c.1732-3T>C
NM_001258273.2:c.1009-3T>C
NM_001258274.3:c.1009-3T>C
NM_001354615.2:c.1009-3T>C
NM_001354616.2:c.1009-3T>C
NM_001354617.2:c.1009-3T>C
NM_001354618.2:c.1009-3T>C
NM_001354619.2:c.1009-3T>C
NM_001354620.2:c.1438-3T>C
NM_001354621.2:c.709-3T>C
NM_001354622.2:c.709-3T>C
NM_001354623.2:c.709-3T>C
NM_001354624.2:c.658-3T>C
NM_001354625.2:c.658-3T>C
NM_001354626.2:c.658-3T>C
NM_001354627.2:c.658-3T>C
NM_001354628.2:c.1732-3T>C
NM_001354629.2:c.1633-3T>C
NM_001354630.2:c.1732-1001T>C
LRG_216t1:c.1732-3T>C
LRG_216:g.59167T>C
NC_000003.11:g.37089007T>C
NM_000249.3:c.1732-3T>C

Links:

dbSNP: rs1207710123

NCBI 1000 Genomes Browser:

rs1207710123

Molecular consequence:

NM_000249.4:c.1732-3T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001167617.3:c.1438-3T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001167618.3:c.1009-3T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001167619.3:c.1009-3T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001258271.2:c.1732-3T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001258273.2:c.1009-3T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001258274.3:c.1009-3T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001354615.2:c.1009-3T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001354616.2:c.1009-3T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001354617.2:c.1009-3T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001354618.2:c.1009-3T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001354619.2:c.1009-3T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001354620.2:c.1438-3T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001354621.2:c.709-3T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001354622.2:c.709-3T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001354623.2:c.709-3T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001354624.2:c.658-3T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001354625.2:c.658-3T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001354626.2:c.658-3T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001354627.2:c.658-3T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001354628.2:c.1732-3T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001354629.2:c.1633-3T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001354630.2:c.1732-1001T>C - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Hereditary nonpolyposis colorectal neoplasms
Identifiers:: MeSH: D003123; MedGen: C0009405

Recent activity

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Homo sapiens lysophosphatidic acid receptor 1 (LPAR1), transcript variant 60, mR...
Homo sapiens lysophosphatidic acid receptor 1 (LPAR1), transcript variant 60, mRNA
gi|1913867742|ref|NM_001387505.1|

Nucleotide
Homo sapiens lysophosphatidic acid receptor 1 (LPAR1), transcript variant 58, mR...
Homo sapiens lysophosphatidic acid receptor 1 (LPAR1), transcript variant 58, mRNA
gi|1914178165|ref|NM_001387503.1|

Nucleotide
lysophosphatidic acid receptor 1 isoform a [Homo sapiens]
lysophosphatidic acid receptor 1 isoform a [Homo sapiens]
gi|1914210376|ref|NP_001374440.1|

Protein
Homo sapiens lysophosphatidic acid receptor 1 (LPAR1), transcript variant 67, mR...
Homo sapiens lysophosphatidic acid receptor 1 (LPAR1), transcript variant 67, mRNA
gi|1916745599|ref|NM_001387512.1|

Nucleotide
Homo sapiens lysophosphatidic acid receptor 1 (LPAR1), transcript variant 36, mR...
Homo sapiens lysophosphatidic acid receptor 1 (LPAR1), transcript variant 36, mRNA
gi|1913867820|ref|NM_001387479.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001535032	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Apr 19, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 17576681, 9536098, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001535032

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Apr 19, 2022)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

Buratti E, Chivers M, Královicová J, Romano M, Baralle M, Krainer AR, Vorechovsky I.

Nucleic Acids Res. 2007;35(13):4250-63. Epub 2007 Jun 18.

PubMed [citation]

PMID:: 17576681
PMCID:: PMC1934990

Statistical features of human exons and their flanking regions.

Zhang MQ.

Hum Mol Genet. 1998 May;7(5):919-32.

PubMed [citation]

PMID:: 9536098

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001535032.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change falls in intron 15 of the MLH1 gene. It does not directly change the encoded amino acid sequence of the MLH1 protein. It affects a nucleotide within the consensus splice site. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with MLH1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1037949). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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

Last Updated: Sep 29, 2024

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