NM_000116.5(TAFAZZIN):c.253C>T (p.Arg85Cys) AND 3-Methylglutaconic aciduria type 2

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 28, 2024
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:: RCV001036319.5

Allele description [Variation Report for NM_000116.5(TAFAZZIN):c.253C>T (p.Arg85Cys)]

NM_000116.5(TAFAZZIN):c.253C>T (p.Arg85Cys)

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.253C>T (p.Arg85Cys)

HGVS:

NC_000023.11:g.154413221C>T
NG_009634.2:g.6687C>T
NG_012884.2:g.3868G>A
NM_000116.5:c.253C>TMANE SELECT
NM_001303465.2:c.307C>T
NM_181311.4:c.253C>T
NM_181312.4:c.253C>T
NM_181313.4:c.253C>T
NP_000107.1:p.Arg85Cys
NP_001290394.1:p.Arg103Cys
NP_851828.1:p.Arg85Cys
NP_851829.1:p.Arg85Cys
NP_851830.1:p.Arg85Cys
LRG_131t1:c.253C>T
LRG_131:g.6687C>T
LRG_131p1:p.Arg85Cys
NC_000023.10:g.153641558C>T
NG_009634.1:g.6682C>T
NM_000116.4:c.253C>T
NR_024048.3:n.558C>T

Protein change:

R103C

Links:

dbSNP: rs376769286

NCBI 1000 Genomes Browser:

rs376769286

Molecular consequence:

NM_000116.5:c.253C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001303465.2:c.307C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_181311.4:c.253C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_181312.4:c.253C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_181313.4:c.253C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_024048.3:n.558C>T - 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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Trnar-acg [Bicyclus anynana]
Trnar-acg [Bicyclus anynana]
Gene ID:112050738

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001199674	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 28, 2024)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 29247119, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001199674

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 28, 2024)

germline

clinical testing

PubMed (2)
[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

Applying High-Resolution Variant Classification to Cardiac Arrhythmogenic Gene Testing in a Demographically Diverse Cohort of Sudden Unexplained Deaths.

Lin Y, Williams N, Wang D, Coetzee W, Zhou B, Eng LS, Um SY, Bao R, Devinsky O, McDonald TV, Sampson BA, Tang Y.

Circ Cardiovasc Genet. 2017 Dec;10(6). doi:pii: e001839. 10.1161/CIRCGENETICS.117.001839.

PubMed [citation]

PMID:: 29247119

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, SCV001199674.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 85 of the TAZ protein (p.Arg85Cys). This variant is present in population databases (rs376769286, gnomAD 0.004%). This missense change has been observed in individual(s) with sudden unexplained death (PMID: 29247119). ClinVar contains an entry for this variant (Variation ID: 835434). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. 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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