NM_000116.5(TAFAZZIN):c.700-1del AND 3-Methylglutaconic aciduria type 2

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Dec 11, 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:: RCV003512474.1

Allele description [Variation Report for NM_000116.5(TAFAZZIN):c.700-1del]

NM_000116.5(TAFAZZIN):c.700-1del

Gene:

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

Variant type:

Deletion

Cytogenetic location:

Xq28

Genomic location:

Preferred name:

NM_000116.5(TAFAZZIN):c.700-1del

HGVS:

NC_000023.11:g.154420657del
NG_009634.2:g.14123del
NG_147843.1:g.668del
NM_000116.5:c.700-1delMANE SELECT
NM_001303465.2:c.712-1del
NM_001410698.1:c.664-1del
NM_181311.4:c.610-1del
NM_181312.4:c.658-1del
NM_181313.4:c.568-1del
LRG_131t1:c.700-1del
LRG_131:g.14123del
NC_000023.10:g.153648996del

Molecular consequence:

NM_000116.5:c.700-1del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001303465.2:c.712-1del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001410698.1:c.664-1del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_181311.4:c.610-1del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_181312.4:c.658-1del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_181313.4:c.568-1del - splice acceptor variant - [Sequence Ontology: SO:0001574]

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
SCV004324679	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely pathogenic (Dec 11, 2023)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 16199547, 16427346, 22382802, 23409742, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004324679

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely pathogenic
(Dec 11, 2023)

germline

clinical testing

PubMed (5)
[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

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]

PMID:: 16199547
PMCID:: PMC1735933

Genetic analysis in patients with left ventricular noncompaction and evidence for genetic heterogeneity.

Xing Y, Ichida F, Matsuoka T, Isobe T, Ikemoto Y, Higaki T, Tsuji T, Haneda N, Kuwabara A, Chen R, Futatani T, Tsubata S, Watanabe S, Watanabe K, Hirono K, Uese K, Miyawaki T, Bowles KR, Bowles NE, Towbin JA.

Mol Genet Metab. 2006 May;88(1):71-7. Epub 2006 Jan 19.

PubMed [citation]

PMID:: 16427346

See all PubMed Citations (5)

Details of each submission

From Invitae, SCV004324679.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

This sequence change affects a splice site in intron 9 of the TAZ gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in TAZ are known to be pathogenic (PMID: 16427346, 22382802, 23409742). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with TAZ-related conditions. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

#	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: Feb 20, 2024

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