rs1553144065

Positions:

• chr1-12002085-TGGC-T

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM1 PM2 PM4_Supporting

The NM_014874.4(MFN2):​c.1146_1148del​(p.Ala383del) variant causes a inframe deletion change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: MFN2 NM_014874.4 inframe_deletion
• Clinical Significance: Uncertain significance criteria provided, multiple submitters, no conflicts U:2
• Conservation: PhyloP100: 5.84

Genes affected

MFN2 (HGNC:16877): (mitofusin 2) This gene encodes a mitochondrial membrane protein that participates in mitochondrial fusion and contributes to the maintenance and operation of the mitochondrial network. This protein is involved in the regulation of vascular smooth muscle cell proliferation, and it may play a role in the pathophysiology of obesity. Mutations in this gene cause Charcot-Marie-Tooth disease type 2A2, and hereditary motor and sensory neuropathy VI, which are both disorders of the peripheral nervous system. Defects in this gene have also been associated with early-onset stroke. Two transcript variants encoding the same protein have been identified. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 5 ACMG points.

• PM1: In a region_of_interest Part of a helix bundle domain, formed by helices from N-terminal and C-terminal regions (size 26) in uniprot entity MFN2_HUMAN there are 21 pathogenic changes around while only 0 benign (100%) in NM_014874.4
• PM2: Very rare variant in population databases, with high coverage
• PM4: Nonframeshift variant in NON repetitive region in NM_014874.4. Strenght limited to Supporting due to length of the change: 1aa.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MFN2	NM_014874.4	c.1146_1148del	p.Ala383del	inframe_deletion	11/19	ENST00000235329.10	NP_055689.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MFN2	ENST00000235329.10	c.1146_1148del	p.Ala383del	inframe_deletion	11/19	1	NM_014874.4	ENSP00000235329	P1

Frequencies

GnomAD3 genomes Cov.: 33

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 33

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Athena Diagnostics

Feb 18, 2020

- -

Neuropathy, hereditary motor and sensory, type 6A Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Department Of Genetics, Lifeline Super Speciality Hospital, Adoor.

Sep 21, 2017

The patient is with clinical indications of distal sensory neuropathy, neuropathic tremor, bilateral pyramidal signs, and MRI revealed lacunar infarct trigone. Patient was diagnosed to be affected with hereditary sensory motor neuropathy type 5 and has been evaluated for pathogenic variations in the gene MFN2. A heterozygous three base pair deletion in exon 11 of the MFN2 gene (chr1:12062143_12062145delGGC) that results in an in-frame deletion of amino acid Alanine at codon 383 (p.Ala383del;ENST00000235329) was detected. -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1553144065; hg19: chr1-12062142;