NM_020686.6(ABAT):c.1192A>C (p.Ile398Leu) AND Gamma-aminobutyric acid transaminase deficiency

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 15, 2021
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:: RCV001936540.3

Allele description [Variation Report for NM_020686.6(ABAT):c.1192A>C (p.Ile398Leu)]

NM_020686.6(ABAT):c.1192A>C (p.Ile398Leu)

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.1192A>C (p.Ile398Leu)

HGVS:

NC_000016.10:g.8776413A>C
NG_008432.1:g.106827A>C
NM_000663.5:c.1192A>C
NM_001127448.2:c.1192A>C
NM_001386600.1:c.1192A>C
NM_001386601.1:c.1192A>C
NM_001386602.1:c.1192A>C
NM_001386603.1:c.1192A>C
NM_001386604.1:c.1192A>C
NM_001386605.1:c.1153A>C
NM_001386606.1:c.1129A>C
NM_001386607.1:c.1129A>C
NM_001386608.1:c.1099A>C
NM_001386609.1:c.1192A>C
NM_001386610.1:c.1057A>C
NM_001386611.1:c.1057A>C
NM_001386612.1:c.994A>C
NM_001386613.1:c.994A>C
NM_001386614.1:c.946A>C
NM_001386615.1:c.1288A>C
NM_001386616.1:c.1192A>C
NM_020686.6:c.1192A>CMANE SELECT
NP_000654.2:p.Ile398Leu
NP_001120920.1:p.Ile398Leu
NP_001373529.1:p.Ile398Leu
NP_001373530.1:p.Ile398Leu
NP_001373531.1:p.Ile398Leu
NP_001373532.1:p.Ile398Leu
NP_001373533.1:p.Ile398Leu
NP_001373534.1:p.Ile385Leu
NP_001373535.1:p.Ile377Leu
NP_001373536.1:p.Ile377Leu
NP_001373537.1:p.Ile367Leu
NP_001373538.1:p.Ile398Leu
NP_001373539.1:p.Ile353Leu
NP_001373540.1:p.Ile353Leu
NP_001373541.1:p.Ile332Leu
NP_001373542.1:p.Ile332Leu
NP_001373543.1:p.Ile316Leu
NP_001373544.1:p.Ile430Leu
NP_001373545.1:p.Ile398Leu
NP_065737.2:p.Ile398Leu
NC_000016.9:g.8870270A>C

Protein change:

I316L

Links:

dbSNP: rs2060264213

NCBI 1000 Genomes Browser:

rs2060264213

Molecular consequence:

NM_000663.5:c.1192A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001127448.2:c.1192A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001386600.1:c.1192A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001386601.1:c.1192A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001386602.1:c.1192A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001386603.1:c.1192A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001386604.1:c.1192A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001386605.1:c.1153A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001386606.1:c.1129A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001386607.1:c.1129A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001386608.1:c.1099A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001386609.1:c.1192A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001386610.1:c.1057A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001386611.1:c.1057A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001386612.1:c.994A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001386613.1:c.994A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001386614.1:c.946A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001386615.1:c.1288A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001386616.1:c.1192A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_020686.6:c.1192A>C - 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
SCV002203659	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 15, 2021)	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

SCV002203659

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 15, 2021)

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, SCV002203659.3

#	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 isoleucine, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 398 of the ABAT protein (p.Ile398Leu). 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. 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. This variant has not been reported in the literature in individuals affected with ABAT-related conditions. This variant is not present in population databases (gnomAD no frequency).

#	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

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