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NM_000249.4(MLH1):c.1038+1G>C AND Colorectal cancer, hereditary nonpolyposis, type 2

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jul 19, 2023
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:
RCV003450998.1

Allele description [Variation Report for NM_000249.4(MLH1):c.1038+1G>C]

NM_000249.4(MLH1):c.1038+1G>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.1038+1G>C
HGVS:
  • NC_000003.12:g.37020464G>C
  • NG_007109.2:g.32115G>C
  • NM_000249.4:c.1038+1G>CMANE SELECT
  • NM_001167617.3:c.744+1G>C
  • NM_001167618.3:c.315+1G>C
  • NM_001167619.3:c.315+1G>C
  • NM_001258271.2:c.1038+1G>C
  • NM_001258273.2:c.315+1G>C
  • NM_001258274.3:c.315+1G>C
  • NM_001354615.2:c.315+1G>C
  • NM_001354616.2:c.315+1G>C
  • NM_001354617.2:c.315+1G>C
  • NM_001354618.2:c.315+1G>C
  • NM_001354619.2:c.315+1G>C
  • NM_001354620.2:c.744+1G>C
  • NM_001354621.2:c.15+1G>C
  • NM_001354622.2:c.15+1G>C
  • NM_001354623.2:c.15+1G>C
  • NM_001354624.2:c.-36-5173G>C
  • NM_001354625.2:c.-36-5173G>C
  • NM_001354626.2:c.-36-5173G>C
  • NM_001354627.2:c.-36-5173G>C
  • NM_001354628.2:c.1038+1G>C
  • NM_001354629.2:c.939+1G>C
  • NM_001354630.2:c.1038+1G>C
  • LRG_216t1:c.1038+1G>C
  • LRG_216:g.32115G>C
  • NC_000003.11:g.37061955G>C
  • NM_000249.3:c.1038+1G>C
Links:
dbSNP: rs267607816
NCBI 1000 Genomes Browser:
rs267607816
Molecular consequence:
  • NM_001354624.2:c.-36-5173G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354625.2:c.-36-5173G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354626.2:c.-36-5173G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354627.2:c.-36-5173G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000249.4:c.1038+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001167617.3:c.744+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001167618.3:c.315+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001167619.3:c.315+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001258271.2:c.1038+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001258273.2:c.315+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001258274.3:c.315+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354615.2:c.315+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354616.2:c.315+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354617.2:c.315+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354618.2:c.315+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354619.2:c.315+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354620.2:c.744+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354621.2:c.15+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354622.2:c.15+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354623.2:c.15+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354628.2:c.1038+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354629.2:c.939+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001354630.2:c.1038+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]

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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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV004187046Myriad Genetics, Inc.
criteria provided, single submitter

(Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))
Likely pathogenic
(Jul 19, 2023)
unknownclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Myriad Genetics, Inc., SCV004187046.1

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

Description

This variant is considered likely pathogenic. This variant occurs within a consensus splice junction and is predicted to result in abnormal mRNA splicing of either an out-of-frame exon or an in-frame exon necessary for protein stability and/or normal function.

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

Last Updated: Jun 9, 2024