NC_000016.9:g.(?_8851594)_(8941702_?)dup AND Gamma-aminobutyric acid transaminase deficiency

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 28, 2018
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:: RCV000817955.2

Allele description [Variation Report for NC_000016.9:g.(?_8851594)_(8941702_?)dup]

NC_000016.9:g.(?_8851594)_(8941702_?)dup

Genes:

ABAT:4-aminobutyrate aminotransferase [Gene - OMIM - HGNC]
LOC130058390:ATAC-STARR-seq lymphoblastoid silent region 7177 [Gene]
LOC130058391:ATAC-STARR-seq lymphoblastoid silent region 7178 [Gene]
LOC130058392:ATAC-STARR-seq lymphoblastoid silent region 7179 [Gene]
LOC130058393:ATAC-STARR-seq lymphoblastoid silent region 7180 [Gene]
PMM2:phosphomannomutase 2 [Gene - OMIM - HGNC]
TMEM186:transmembrane protein 186 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

16p13.2

Genomic location:

Preferred name:

NC_000016.9:g.(?_8851594)_(8941702_?)dup

HGVS:

NC_000016.9:g.(?_8851594)_(8941702_?)dup

Condition(s)

Name:: Gamma-aminobutyric acid transaminase deficiency (GABATD)
Synonyms:: GABA transaminase deficiency; Gamma aminobutyrate transaminase deficiency; 4 alpha aminobutyrate transaminase deficiency; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0013166; MedGen: C0342708; Orphanet: 2066; OMIM: 613163

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000958542	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 28, 2018)	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

SCV000958542

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 28, 2018)

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, SCV000958542.1

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

Description

This variant results in a copy number gain of the genomic region encompassing exons 6-16 of the ABAT gene. The 5' boundary is likely confined to intron 5. The 3' end of this event is unknown as it extends beyond the assayed region for this gene and therefore may encompass additional genes. As the precise location of this event is unknown, it may be in tandem or it may be located elsewhere in the genome. This variant has not been reported in the literature in individuals with ABAT-related disease. Experimental studies and prediction algorithms are not available for this variant, and the functional significance of the affected amino acid(s) is currently unknown. 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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