NM_001127644.2(GABRA1):c.641G>A (p.Arg214His) AND Developmental and epileptic encephalopathy, 19

Germline classification:: Pathogenic/Likely pathogenic (5 submissions)
Last evaluated:: May 10, 2023
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:: RCV000417089.7

Allele description [Variation Report for NM_001127644.2(GABRA1):c.641G>A (p.Arg214His)]

NM_001127644.2(GABRA1):c.641G>A (p.Arg214His)

Gene:

GABRA1:gamma-aminobutyric acid type A receptor subunit alpha1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

5q34

Genomic location:

Preferred name:

NM_001127644.2(GABRA1):c.641G>A (p.Arg214His)

HGVS:

NC_000005.10:g.161882639G>A
NG_011548.1:g.40449G>A
NM_000806.5:c.641G>A
NM_001127643.2:c.641G>A
NM_001127644.2:c.641G>AMANE SELECT
NM_001127645.2:c.641G>A
NM_001127648.2:c.641G>A
NP_000797.2:p.Arg214His
NP_001121115.1:p.Arg214His
NP_001121116.1:p.Arg214His
NP_001121117.1:p.Arg214His
NP_001121120.1:p.Arg214His
NC_000005.9:g.161309645G>A
NM_001127644.2:c.641G>A
NM_001127648.1:c.641G>A
p.(Arg214His)
p.R214H

Protein change:

R214H

Links:

dbSNP: rs886039373

NCBI 1000 Genomes Browser:

rs886039373

Molecular consequence:

NM_000806.5:c.641G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001127643.2:c.641G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001127644.2:c.641G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001127645.2:c.641G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001127648.2:c.641G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Developmental and epileptic encephalopathy, 19 (DEE19)
Synonyms:: Epileptic encephalopathy, early infantile, 19
Identifiers:: MONDO: MONDO:0014328; MedGen: C3810400; Orphanet: 33069; OMIM: 615744

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000494656	Center of Genomic medicine, Geneva, University Hospital of Geneva	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jul 5, 2016)	de novo	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001160787	Cavalleri Lab, Royal College of Surgeons in Ireland	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Dec 11, 2019)	de novo	research	PubMed (2) [See all records that cite these PMIDs] 25741868, 32238909
SCV001193765	Genatak	no assertion criteria provided	Pathogenic (Jun 23, 2018)	de novo	clinical testing
SCV002570057	Center of Excellence for Medical Genomics, Chulalongkorn University	no assertion criteria provided	Pathogenic (Sep 8, 2002)	unknown	research
SCV003924016	Clinical Genetics Laboratory, Skane University Hospital Lund	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (May 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	unknown	yes	not provided	not provided	not provided	not provided	not provided	research
not provided	de novo	yes	1	not provided	not provided	not provided	not provided	clinical testing, research
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A comparison of genomic diagnostics in adults and children with epilepsy and comorbid intellectual disability.

Benson KA, White M, Allen NM, Byrne S, Carton R, Comerford E, Costello D, Doherty C, Dunleavey B, El-Naggar H, Gangadharan N, Heavin S, Kearney H, Lench NJ, Lynch J, McCormack M, Regan MO, Podesta K, Power K, Rogers AS, Steward CA, Sweeney B, et al.

Eur J Hum Genet. 2020 Aug;28(8):1066-1077. doi: 10.1038/s41431-020-0610-3. Epub 2020 Apr 1.

PubMed [citation]

PMID:: 32238909
PMCID:: PMC7381648

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 Center of Genomic medicine, Geneva, University Hospital of Geneva, SCV000494656.2

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

#	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		not provided	not provided	not provided	not provided
2	de novo	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Cavalleri Lab, Royal College of Surgeons in Ireland, SCV001160787.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	research	PubMed (2)

Description

ACMG evidence PS2, PM2, PP2, PP3, PP5

#	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		not provided	not provided	not provided	not provided

From Genatak, SCV001193765.1

#	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 Center of Excellence for Medical Genomics, Chulalongkorn University, SCV002570057.1

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

#	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 Clinical Genetics Laboratory, Skane University Hospital Lund, SCV003924016.1

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

Description

PS3, PS4, PM2, PP3

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

Last Updated: Oct 20, 2024

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