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NM_014874.4(MFN2):c.179C>T (p.Thr60Met)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(1);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Feb 20, 2020)
Last evaluated:
Sep 19, 2019
Accession:
VCV000246508.4
Variation ID:
246508
Description:
single nucleotide variant
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NM_014874.4(MFN2):c.179C>T (p.Thr60Met)

Allele ID
244186
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1p36.22
Genomic location
1: 11992558 (GRCh38) GRCh38 UCSC
1: 12052615 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_255:g.17378C>T
LRG_255t1:c.179C>T LRG_255p1:p.Thr60Met
NM_014874.3:c.179C>T NP_055689.1:p.Thr60Met missense
... more HGVS
Protein change
T60M
Other names
-
Canonical SPDI
NC_000001.11:11992557:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00040 (T)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00006
The Genome Aggregation Database (gnomAD), exomes 0.00005
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00015
1000 Genomes Project 0.00040
The Genome Aggregation Database (gnomAD) 0.00003
Trans-Omics for Precision Medicine (TOPMed) 0.00004
Links
ClinGen: CA598770
dbSNP: rs138345244
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Mar 28, 2016 RCV000236416.1
Benign 1 criteria provided, single submitter Jan 13, 2018 RCV000275642.2
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Sep 19, 2019 RCV000653930.5
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
MFN2 No evidence available No evidence available GRCh38
GRCh37
771 818

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Mar 28, 2016)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000294093.10
Submitted: (Jan 29, 2019)
Evidence details
Comment:
The T60M variant has notbeen published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge.The T60M variant was … (more)
Likely benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Charcot-Marie-Tooth disease, type 2
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000347972.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Hereditary motor and sensory neuropathy with optic atrophy
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000347973.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Uncertain significance
(Sep 19, 2019)
criteria provided, single submitter
Method: clinical testing
Charcot-Marie-Tooth disease, type 2
Allele origin: germline
Invitae
Accession: SCV000775820.3
Submitted: (Feb 06, 2020)
Evidence details
Publications
PubMed (1)
Comment:
This sequence change replaces threonine with methionine at codon 60 of the MFN2 protein (p.Thr60Met). The threonine residue is highly conserved and there is a … (more)

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
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532

Text-mined citations for rs138345244...

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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 24, 2021