NM_000249.4(MLH1):c.1693A>T (p.Ile565Phe) AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Jul 22, 2022
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:: RCV000160538.24

Allele description

NM_000249.4(MLH1):c.1693A>T (p.Ile565Phe)

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.1693A>T (p.Ile565Phe)

Other names:

p.I565F:ATT>TTT

HGVS:

NC_000003.12:g.37042293A>T
NG_007109.2:g.53944A>T
NM_000249.4:c.1693A>TMANE SELECT
NM_001167617.3:c.1399A>T
NM_001167618.3:c.970A>T
NM_001167619.3:c.970A>T
NM_001258271.2:c.1693A>T
NM_001258273.2:c.970A>T
NM_001258274.3:c.970A>T
NM_001354615.2:c.970A>T
NM_001354616.2:c.970A>T
NM_001354617.2:c.970A>T
NM_001354618.2:c.970A>T
NM_001354619.2:c.970A>T
NM_001354620.2:c.1399A>T
NM_001354621.2:c.670A>T
NM_001354622.2:c.670A>T
NM_001354623.2:c.670A>T
NM_001354624.2:c.619A>T
NM_001354625.2:c.619A>T
NM_001354626.2:c.619A>T
NM_001354627.2:c.619A>T
NM_001354628.2:c.1693A>T
NM_001354629.2:c.1594A>T
NM_001354630.2:c.1693A>T
NP_000240.1:p.Ile565Phe
NP_000240.1:p.Ile565Phe
NP_001161089.1:p.Ile467Phe
NP_001161090.1:p.Ile324Phe
NP_001161091.1:p.Ile324Phe
NP_001245200.1:p.Ile565Phe
NP_001245202.1:p.Ile324Phe
NP_001245203.1:p.Ile324Phe
NP_001341544.1:p.Ile324Phe
NP_001341545.1:p.Ile324Phe
NP_001341546.1:p.Ile324Phe
NP_001341547.1:p.Ile324Phe
NP_001341548.1:p.Ile324Phe
NP_001341549.1:p.Ile467Phe
NP_001341550.1:p.Ile224Phe
NP_001341551.1:p.Ile224Phe
NP_001341552.1:p.Ile224Phe
NP_001341553.1:p.Ile207Phe
NP_001341554.1:p.Ile207Phe
NP_001341555.1:p.Ile207Phe
NP_001341556.1:p.Ile207Phe
NP_001341557.1:p.Ile565Phe
NP_001341558.1:p.Ile532Phe
NP_001341559.1:p.Ile565Phe
LRG_216t1:c.1693A>T
LRG_216:g.53944A>T
LRG_216p1:p.Ile565Phe
NC_000003.11:g.37083784A>T
NM_000249.3:c.1693A>T
P40692:p.Ile565Phe

Protein change:

I207F

Links:

UniProtKB: P40692#VAR_012923; dbSNP: rs63750062

NCBI 1000 Genomes Browser:

rs63750062

Molecular consequence:

NM_000249.4:c.1693A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001167617.3:c.1399A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001167618.3:c.970A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001167619.3:c.970A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001258271.2:c.1693A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001258273.2:c.970A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001258274.3:c.970A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354615.2:c.970A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354616.2:c.970A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354617.2:c.970A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354618.2:c.970A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354619.2:c.970A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354620.2:c.1399A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354621.2:c.670A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354622.2:c.670A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354623.2:c.670A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354624.2:c.619A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354625.2:c.619A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354626.2:c.619A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354627.2:c.619A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354628.2:c.1693A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354629.2:c.1594A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354630.2:c.1693A>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Mus musculus carnosine N-methyltransferase 1 (Carnmt1), transcript variant 1, mR...
Mus musculus carnosine N-methyltransferase 1 (Carnmt1), transcript variant 1, mRNA
gi|1783384279|ref|NM_026120.5|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000211112	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Jul 22, 2022)	germline	clinical testing	Citation Link,
SCV001153847	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Uncertain significance (Mar 1, 2019)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000211112

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Jul 22, 2022)

germline

clinical testing

Citation Link,

SCV001153847

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Uncertain significance
(Mar 1, 2019)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000211112.13

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 11093816, 21404117, 18383312, 19015241, 9833759, 15943554, 17510385, 21901500, 23741719, 34426522, 22753075, 12799449, 20533529, 31697235)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From CeGaT Center for Human Genetics Tuebingen, SCV001153847.24

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Jul 15, 2024

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