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NM_000249.4(MLH1):c.1039-1G>A AND not provided

Germline classification:
Pathogenic (4 submissions)
Last evaluated:
Jul 1, 2021
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:
RCV000153506.31

Allele description [Variation Report for NM_000249.4(MLH1):c.1039-1G>A]

NM_000249.4(MLH1):c.1039-1G>A

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.1039-1G>A
HGVS:
  • NC_000003.12:g.37025636G>A
  • NG_007109.2:g.37287G>A
  • NM_000249.4:c.1039-1G>AMANE SELECT
  • NM_001167617.3:c.745-1G>A
  • NM_001167618.3:c.316-1G>A
  • NM_001167619.3:c.316-1G>A
  • NM_001258271.2:c.1039-1G>A
  • NM_001258273.2:c.316-1G>A
  • NM_001258274.3:c.316-1G>A
  • NM_001354615.2:c.316-1G>A
  • NM_001354616.2:c.316-1G>A
  • NM_001354617.2:c.316-1G>A
  • NM_001354618.2:c.316-1G>A
  • NM_001354619.2:c.316-1G>A
  • NM_001354620.2:c.745-1G>A
  • NM_001354621.2:c.16-1G>A
  • NM_001354622.2:c.16-1G>A
  • NM_001354623.2:c.16-1G>A
  • NM_001354624.2:c.-36-1G>A
  • NM_001354625.2:c.-36-1G>A
  • NM_001354626.2:c.-36-1G>A
  • NM_001354627.2:c.-36-1G>A
  • NM_001354628.2:c.1039-1G>A
  • NM_001354629.2:c.940-1G>A
  • NM_001354630.2:c.1039-1G>A
  • LRG_216t1:c.1039-1G>A
  • LRG_216:g.37287G>A
  • NC_000003.11:g.37067127G>A
  • NM_000249.3:c.1039-1G>A
Links:
dbSNP: rs267607819
NCBI 1000 Genomes Browser:
rs267607819
Molecular consequence:
  • NM_000249.4:c.1039-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001167617.3:c.745-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001167618.3:c.316-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001167619.3:c.316-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001258271.2:c.1039-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001258273.2:c.316-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001258274.3:c.316-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001354615.2:c.316-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001354616.2:c.316-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001354617.2:c.316-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001354618.2:c.316-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001354619.2:c.316-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001354620.2:c.745-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001354621.2:c.16-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001354622.2:c.16-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001354623.2:c.16-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001354624.2:c.-36-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001354625.2:c.-36-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001354626.2:c.-36-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001354627.2:c.-36-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001354628.2:c.1039-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001354629.2:c.940-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001354630.2:c.1039-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
Observations:
2

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000211092GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)		Pathogenic
(Jun 5, 2019) 		germlineclinical testing

Citation Link,

SCV000700694Eurofins Ntd Llc (ga)
criteria provided, single submitter

(EGL Classification Definitions)		Pathogenic
(Feb 24, 2014) 		germlineclinical testing

Citation Link,

SCV002017498Revvity Omics, Revvity
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Aug 19, 2019) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV002563756CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)		Pathogenic
(Jul 1, 2021) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing
not providedgermlineunknown1not providednot providednot providednot providedclinical testing

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 GeneDx, SCV000211092.11

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Canonical splice site variant in a gene for which loss-of-function is a known mechanism of disease; Not observed in large population cohorts (Lek et al., 2016); Reported as pathogenic in ClinVar but additional evidence is not available; This variant is associated with the following publications: (PMID: 11306449, 11854177, 10200055, 26681312, 9322509, 11507050, 14574010, 23716351, 10793088, 29296220)

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Eurofins Ntd Llc (ga), SCV000700694.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

From Revvity Omics, Revvity, SCV002017498.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From CeGaT Center for Human Genetics Tuebingen, SCV002563756.16

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Oct 20, 2024