NM_006796.3(AFG3L2):c.2155_2156del (p.Lys719fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 1, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV003568260.2

Allele description [Variation Report for NM_006796.3(AFG3L2):c.2155_2156del (p.Lys719fs)]

NM_006796.3(AFG3L2):c.2155_2156del (p.Lys719fs)

Gene:

AFG3L2:AFG3 like matrix AAA peptidase subunit 2 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

18p11.21

Genomic location:

Preferred name:

NM_006796.3(AFG3L2):c.2155_2156del (p.Lys719fs)

HGVS:

NC_000018.10:g.12337362_12337363del
NG_023361.1:g.44916_44917del
NM_006796.3:c.2155_2156delMANE SELECT
NP_006787.2:p.Lys719Glufs
NP_006787.2:p.Lys719fs
LRG_666t1:c.2153_2154del
LRG_666:g.44916_44917del
LRG_666p1:p.Lys719Glufs
NC_000018.9:g.12337359_12337360del
NC_000018.9:g.12337361_12337362del
NM_006796.2:c.2153_2154delAA

Protein change:

K719fs

Molecular consequence:

NM_006796.3:c.2155_2156del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004307845	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 1, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 31111429, 34333379, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004307845

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 1, 2023)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Spinocerebellar Ataxia Type 28-Phenotypic and Molecular Characterization of a Family with Heterozygous and Compound-Heterozygous Mutations in AFG3L2.

Tunc S, Dulovic-Mahlow M, Baumann H, Baaske MK, Jahn M, Junker J, Münchau A, Brüggemann N, Lohmann K.

Cerebellum. 2019 Aug;18(4):817-822. doi: 10.1007/s12311-019-01036-2.

PubMed [citation]

PMID:: 31111429

Expanding the phenotype of AFG3L2 mutations: Late-onset autosomal recessive spinocerebellar ataxia.

Chiang HL, Fuh JL, Tsai YS, Soong BW, Liao YC, Lee YC.

J Neurol Sci. 2021 Sep 15;428:117600. doi: 10.1016/j.jns.2021.117600. Epub 2021 Jul 27.

PubMed [citation]

PMID:: 34333379

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004307845.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This variant is present in population databases (no rsID available, gnomAD 0.007%). For these reasons, this variant has been classified as Pathogenic. This variant disrupts a region of the AFG3L2 protein in which other variant(s) (p.Val723Met) have been determined to be pathogenic (PMID: 31111429, 34333379). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. This variant has not been reported in the literature in individuals affected with AFG3L2-related conditions. This sequence change creates a premature translational stop signal (p.Lys719Glufs*3) in the AFG3L2 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 79 amino acid(s) of the AFG3L2 protein.

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

Last Updated: Sep 29, 2024

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