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NM_000249.4(MLH1):c.37G>A (p.Glu13Lys) AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 2, 2022
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV003150964.2

Allele description [Variation Report for NM_000249.4(MLH1):c.37G>A (p.Glu13Lys)]

NM_000249.4(MLH1):c.37G>A (p.Glu13Lys)

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.37G>A (p.Glu13Lys)
HGVS:
  • NC_000003.12:g.36993584G>A
  • NG_007109.2:g.5235G>A
  • NG_008418.1:g.4721C>T
  • NM_000249.4:c.37G>AMANE SELECT
  • NM_001167617.3:c.-480G>A
  • NM_001167618.3:c.-909G>A
  • NM_001167619.3:c.-822G>A
  • NM_001258271.2:c.37G>A
  • NM_001258273.2:c.-596G>A
  • NM_001258274.3:c.-1059G>A
  • NM_001354615.2:c.-590G>A
  • NM_001354616.2:c.-590G>A
  • NM_001354617.2:c.-682G>A
  • NM_001354618.2:c.-914G>A
  • NM_001354619.2:c.-1038G>A
  • NM_001354620.2:c.-248G>A
  • NM_001354621.2:c.-1007G>A
  • NM_001354622.2:c.-1120G>A
  • NM_001354623.2:c.-1029G>A
  • NM_001354624.2:c.-790G>A
  • NM_001354625.2:c.-688G>A
  • NM_001354626.2:c.-785G>A
  • NM_001354627.2:c.-1017G>A
  • NM_001354628.2:c.37G>A
  • NM_001354629.2:c.37G>A
  • NM_001354630.2:c.37G>A
  • NP_000240.1:p.Glu13Lys
  • NP_000240.1:p.Glu13Lys
  • NP_001245200.1:p.Glu13Lys
  • NP_001341557.1:p.Glu13Lys
  • NP_001341558.1:p.Glu13Lys
  • NP_001341559.1:p.Glu13Lys
  • LRG_216t1:c.37G>A
  • LRG_216:g.5235G>A
  • LRG_216p1:p.Glu13Lys
  • NC_000003.11:g.37035075G>A
  • NM_000249.3:c.37G>A
Protein change:
E13K
Links:
dbSNP: rs587779008
NCBI 1000 Genomes Browser:
rs587779008
Molecular consequence:
  • NM_001167617.3:c.-480G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001167618.3:c.-909G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001167619.3:c.-822G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001258273.2:c.-596G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001258274.3:c.-1059G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354615.2:c.-590G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354616.2:c.-590G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354617.2:c.-682G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354618.2:c.-914G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354619.2:c.-1038G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354620.2:c.-248G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354621.2:c.-1007G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354622.2:c.-1120G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354623.2:c.-1029G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354624.2:c.-790G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354625.2:c.-688G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354626.2:c.-785G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001354627.2:c.-1017G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_000249.4:c.37G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001258271.2:c.37G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354628.2:c.37G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354629.2:c.37G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354630.2:c.37G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003839721Genetic Services Laboratory, University of Chicago
no assertion criteria provided
Uncertain significance
(Sep 2, 2022) 		germlineclinical testing

Help

Summary from all submissions

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

Details of each submission

From Genetic Services Laboratory, University of Chicago, SCV003839721.1

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

Description

DNA sequence analysis of the MLH1 gene demonstrated a sequence change, c.37G>A, in exon 1 that results in an amino acid change, p.Glu13Lys. This sequence change has not been previously described in individuals with MLH1 related disorders.This sequence change has been described in the gnomAD database in one individual which corresponds to a population frequency of 0.0004% (dbSNP rs587779008). The p.Glu13Lys change affects a highly conserved amino acid residue located in a domain of the MLH1 protein that is known to be functional. In-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL) provide contradictory results for the p.Glu13Lys substitution. Due to insufficient evidences and the lack of functional studies, the clinical significance of the p.Glu13Lys change remains unknown at this time.

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

Last Updated: Sep 29, 2024