NM_006796.3(AFG3L2):c.2359A>G (p.Lys787Glu) AND not provided

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

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 21, 2022
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:: RCV002614047.9

Allele description

NM_006796.3(AFG3L2):c.2359A>G (p.Lys787Glu)

Genes:

AFG3L2:AFG3 like matrix AAA peptidase subunit 2 [Gene - OMIM - HGNC]
TUBB6:tubulin beta 6 class V [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

18p11.21

Genomic location:

Preferred name:

NM_006796.3(AFG3L2):c.2359A>G (p.Lys787Glu)

HGVS:

NC_000018.10:g.12329600T>C
NG_023361.1:g.52677A>G
NM_001303525.2:c.*417T>C
NM_006796.3:c.2359A>GMANE SELECT
NP_006787.2:p.Lys787Glu
NP_006787.2:p.Lys787Glu
LRG_666t1:c.2359A>G
LRG_666:g.52677A>G
LRG_666p1:p.Lys787Glu
NC_000018.9:g.12329599T>C
NM_006796.2:c.2359A>G

Protein change:

K787E

Molecular consequence:

NM_001303525.2:c.*417T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_006796.3:c.2359A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

sonic hedgehog protein, partial [Myotis ricketti]
sonic hedgehog protein, partial [Myotis ricketti]
gi|1227426976|gb|ASR18904.1|

Protein
MAG: hypothetical protein AMJ57_00215 [Parcubacteria bacterium SG8_24]
MAG: hypothetical protein AMJ57_00215 [Parcubacteria bacterium SG8_24]
gi|931397140|gb|KPJ86178.1||gnl|WGS |AMJ57_00215

Protein
PREDICTED: Populus trichocarpa tubulin alpha-3 chain (LOC7489664), mRNA
PREDICTED: Populus trichocarpa tubulin alpha-3 chain (LOC7489664), mRNA
gi|2396541020|ref|XM_002319652.4|

Nucleotide
Pyrenochaeta sp. ZLY-2010 strain M139 laccase-like gene, partial sequence
Pyrenochaeta sp. ZLY-2010 strain M139 laccase-like gene, partial sequence
gi|313756299|gb|HM484208.1|

Nucleotide
PREDICTED: Homo sapiens adhesion G protein-coupled receptor B2 (ADGRB2), transcr...
PREDICTED: Homo sapiens adhesion G protein-coupled receptor B2 (ADGRB2), transcript variant X22, mRNA
gi|2462511842|ref|XM_054337883.1|

Nucleotide

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002961564	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 21, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002961564

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 21, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV002961564.2

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

Description

This sequence change replaces lysine, which is basic and polar, with glutamic acid, which is acidic and polar, at codon 787 of the AFG3L2 protein (p.Lys787Glu). This variant is present in population databases (rs761546721, gnomAD 0.004%). This variant has not been reported in the literature in individuals affected with AFG3L2-related conditions. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt AFG3L2 protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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 16, 2024

ClinVar

Relating variation to medicine