NM_003042.4(SLC6A1):c.1084G>A (p.Gly362Arg) AND Myoclonic-astatic epilepsy

Germline classification:: Pathogenic/Likely pathogenic (4 submissions)
Last evaluated:: Sep 15, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV003444555.5

Allele description [Variation Report for NM_003042.4(SLC6A1):c.1084G>A (p.Gly362Arg)]

NM_003042.4(SLC6A1):c.1084G>A (p.Gly362Arg)

Gene:

SLC6A1:solute carrier family 6 member 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3p25.3

Genomic location:

Preferred name:

NM_003042.4(SLC6A1):c.1084G>A (p.Gly362Arg)

HGVS:

NC_000003.12:g.11028740G>A
NG_053003.1:g.41012G>A
NM_001348250.2:c.1084G>A
NM_001348251.2:c.724G>A
NM_001348252.2:c.550G>A
NM_001348253.2:c.550G>A
NM_003042.4:c.1084G>AMANE SELECT
NP_001335179.1:p.Gly362Arg
NP_001335180.1:p.Gly242Arg
NP_001335181.1:p.Gly184Arg
NP_001335182.1:p.Gly184Arg
NP_003033.3:p.Gly362Arg
NC_000003.11:g.11070426G>A
NM_003042.3:c.1084G>A

Protein change:

G184R

Links:

dbSNP: rs1131691302

NCBI 1000 Genomes Browser:

rs1131691302

Molecular consequence:

NM_001348250.2:c.1084G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001348251.2:c.724G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001348252.2:c.550G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001348253.2:c.550G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_003042.4:c.1084G>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Name:: Myoclonic-astatic epilepsy
Synonyms:: Myoclonic atonic seizures; Generalized myoclonic-atonic seizure
Identifiers:: MONDO: MONDO:0016025; MedGen: C0393702; Orphanet: 1942; Human Phenotype Ontology: HP:0011170

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002044464	Institute of Human Genetics, University of Leipzig Medical Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Nov 24, 2021)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002764891	Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München	criteria provided, single submitter (Classification criteria August 2017)	Pathogenic (Mar 26, 2021)	de novo	clinical testing	Citation Link,
SCV003807409	Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Sep 15, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004012835	GenomeConnect - Brain Gene Registry	no classification provided	not provided	de novo	phenotyping only

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	1	not provided	not provided	1	not provided	clinical testing
not provided	unknown	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	de novo	yes	2	not provided	not provided	1	not provided	clinical testing, phenotyping only

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Institute of Human Genetics, University of Leipzig Medical Center, SCV002044464.1

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

Description

_x000D_ Criteria applied: PS2_MOD, PS4_MOD, PM1, PM2_SUP, PP3

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München, SCV002764891.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	de novo	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

From Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein, SCV003807409.1

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

Description

ACMG classification criteria: PS4 moderated, PM1 moderated, PM2 moderated, PP3 supporting

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	1	not provided	not provided		1	not provided	not provided	not provided

From GenomeConnect - Brain Gene Registry, SCV004012835.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	phenotyping only	not provided

Description

Variant interpreted as Likely pathogenic and reported on 05-05-2017 by Lab GeneDx. Assertions are reported exactly as they appear on the patient provided laboratory report. GenomeConnect does not attempt to reinterpret the variant. The IDDRC-CTSA National Brain Gene Registry (BGR) is a study funded by the U.S. National Center for Advancing Translational Sciences (NCATS) and includes 13 Intellectual and Developmental Disability Research Center (IDDRC) institutions. The study is led by Principal Investigator Dr. Philip Payne from Washington University. The BGR is a data commons of gene variants paired with subject clinical information. This database helps scientists learn more about genetic changes and their impact on the brain and behavior. Participation in the Brain Gene Registry requires participation in GenomeConnect. More information about the Brain Gene Registry can be found on the study website - https://braingeneregistry.wustl.edu/.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	de novo	yes	1	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Nov 10, 2024

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