NM_000116.5(TAFAZZIN):c.758G>A (p.Arg253Gln) AND 3-Methylglutaconic aciduria type 2

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 20, 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:: RCV000695963.3

Allele description [Variation Report for NM_000116.5(TAFAZZIN):c.758G>A (p.Arg253Gln)]

NM_000116.5(TAFAZZIN):c.758G>A (p.Arg253Gln)

Gene:

TAFAZZIN:tafazzin, phospholipid-lysophospholipid transacylase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xq28

Genomic location:

Preferred name:

NM_000116.5(TAFAZZIN):c.758G>A (p.Arg253Gln)

HGVS:

NC_000023.11:g.154420716G>A
NG_009634.2:g.14182G>A
NM_000116.5:c.758G>AMANE SELECT
NM_001303465.2:c.770G>A
NM_181311.4:c.668G>A
NM_181312.4:c.716G>A
NM_181313.4:c.626G>A
NP_000107.1:p.Arg253Gln
NP_001290394.1:p.Arg257Gln
NP_851828.1:p.Arg223Gln
NP_851829.1:p.Arg239Gln
NP_851830.1:p.Arg209Gln
LRG_131t1:c.758G>A
LRG_131:g.14182G>A
LRG_131p1:p.Arg253Gln
NC_000023.10:g.153649055G>A
NG_009634.1:g.14179G>A
NM_000116.3:c.758G>A
NM_000116.4:c.758G>A
NR_024048.3:n.1079G>A

Protein change:

R209Q

Links:

dbSNP: rs782653725

NCBI 1000 Genomes Browser:

rs782653725

Molecular consequence:

NM_000116.5:c.758G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001303465.2:c.770G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_181311.4:c.668G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_181312.4:c.716G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_181313.4:c.626G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_024048.3:n.1079G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: 3-Methylglutaconic aciduria type 2 (BTHS)
Synonyms:: Barth syndrome; 3-methylglutaconicaciduria type II; MGA type II; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0010543; MedGen: C0574083; Orphanet: 111; OMIM: 302060

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000824504	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 20, 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

SCV000824504

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 20, 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 Labcorp Genetics (formerly Invitae), Labcorp, SCV000824504.2

#	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 arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 253 of the TAZ protein (p.Arg253Gln). This variant is present in population databases (rs782653725, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with TAZ-related conditions. ClinVar contains an entry for this variant (Variation ID: 234467). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. 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 29, 2024

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