NM_020686.6(ABAT):c.531G>A (p.Met177Ile) AND Gamma-aminobutyric acid transaminase deficiency

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 10, 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:: RCV002991589.2

Allele description [Variation Report for NM_020686.6(ABAT):c.531G>A (p.Met177Ile)]

NM_020686.6(ABAT):c.531G>A (p.Met177Ile)

Gene:

ABAT:4-aminobutyrate aminotransferase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

16p13.2

Genomic location:

Preferred name:

NM_020686.6(ABAT):c.531G>A (p.Met177Ile)

HGVS:

NC_000016.10:g.8764821G>A
NG_008432.1:g.95235G>A
NM_000663.5:c.531G>A
NM_001127448.2:c.531G>A
NM_001386600.1:c.531G>A
NM_001386601.1:c.531G>A
NM_001386602.1:c.531G>A
NM_001386603.1:c.531G>A
NM_001386604.1:c.531G>A
NM_001386605.1:c.531G>A
NM_001386606.1:c.531G>A
NM_001386607.1:c.531G>A
NM_001386608.1:c.447+672G>A
NM_001386609.1:c.531G>A
NM_001386610.1:c.396G>A
NM_001386611.1:c.396G>A
NM_001386612.1:c.396G>A
NM_001386613.1:c.396G>A
NM_001386614.1:c.285G>A
NM_001386615.1:c.627G>A
NM_001386616.1:c.531G>A
NM_020686.6:c.531G>AMANE SELECT
NP_000654.2:p.Met177Ile
NP_001120920.1:p.Met177Ile
NP_001373529.1:p.Met177Ile
NP_001373530.1:p.Met177Ile
NP_001373531.1:p.Met177Ile
NP_001373532.1:p.Met177Ile
NP_001373533.1:p.Met177Ile
NP_001373534.1:p.Met177Ile
NP_001373535.1:p.Met177Ile
NP_001373536.1:p.Met177Ile
NP_001373538.1:p.Met177Ile
NP_001373539.1:p.Met132Ile
NP_001373540.1:p.Met132Ile
NP_001373541.1:p.Met132Ile
NP_001373542.1:p.Met132Ile
NP_001373543.1:p.Met95Ile
NP_001373544.1:p.Met209Ile
NP_001373545.1:p.Met177Ile
NP_065737.2:p.Met177Ile
NC_000016.9:g.8858678G>A

Protein change:

M132I

Molecular consequence:

NM_001386608.1:c.447+672G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_000663.5:c.531G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001127448.2:c.531G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001386600.1:c.531G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001386601.1:c.531G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001386602.1:c.531G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001386603.1:c.531G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001386604.1:c.531G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001386605.1:c.531G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001386606.1:c.531G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001386607.1:c.531G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001386609.1:c.531G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001386610.1:c.396G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001386611.1:c.396G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001386612.1:c.396G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001386613.1:c.396G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001386614.1:c.285G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001386615.1:c.627G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001386616.1:c.531G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_020686.6:c.531G>A - missense variant - [Sequence Ontology: SO:0001583]

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
SCV003302018	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 10, 2023)	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

SCV003302018

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 10, 2023)

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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV003302018.2

#	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 methionine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 177 of the ABAT protein (p.Met177Ile). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with ABAT-related conditions. ClinVar contains an entry for this variant (Variation ID: 2091321). 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 ABAT protein function. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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: May 1, 2024

ClinVar

Relating variation to medicine