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NM_000249.4(MLH1):c.380+2T>C

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Interpretation:
Likely pathogenic​

Review status:
reviewed by expert panel
Submissions:
3 (Most recent: Oct 27, 2021)
Last evaluated:
Jun 21, 2019
Accession:
VCV000090193.4
Variation ID:
90193
Description:
single nucleotide variant
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NM_000249.4(MLH1):c.380+2T>C

Allele ID
95667
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
3p22.2
Genomic location
3: 37004476 (GRCh38) GRCh38 UCSC
3: 37045967 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NM_000249.3:c.380+2T>C splice donor
NC_000003.11:g.37045967T>C
NC_000003.12:g.37004476T>C
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000003.12:37004475:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA010057
dbSNP: rs267607742
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 1 reviewed by expert panel Jun 21, 2019 RCV000075681.3
Pathogenic 2 criteria provided, single submitter Apr 19, 2021 RCV001356725.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
MLH1 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
3503 3539

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Jun 21, 2019)
reviewed by expert panel
Method: curation
Lynch syndrome
Allele origin: germline
International Society for Gastrointestinal Hereditary Tumours (InSiGHT)
Accession: SCV000106684.3
Submitted: (Jun 21, 2019)
Evidence details
Other databases
http://www.insight-database.org/…
Comment:
Interrupts canonical donor splice site
Pathogenic
(Apr 19, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001983877.1
Submitted: (Oct 27, 2021)
Evidence details
Comment:
Canonical splice site variant predicted to result in a null allele in a gene for which loss-of-function is a known mechanism of disease; Observed in … (more)
Uncertain significance
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: unknown
Department of Pathology and Laboratory Medicine,Sinai Health System
Additional submitter:
Franklin by Genoox
Study: The Canadian Open Genetics Repository (COGR)
Accession: SCV001551969.1
Submitted: (Mar 31, 2021)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
http://www.insight-database.org/classifications/?gene=MLH1&variant=c.380+2T%3EC - - - -

Text-mined citations for rs267607742...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 30, 2021