NM_000171.4(GLRA1):c.477-1G>A AND Hyperekplexia 1

Germline classification:: Pathogenic (1 submission)
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:: RCV000576251.2

Allele description [Variation Report for NM_000171.4(GLRA1):c.477-1G>A]

NM_000171.4(GLRA1):c.477-1G>A

Gene:

GLRA1:glycine receptor alpha 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

5q33.1

Genomic location:

Preferred name:

NM_000171.4(GLRA1):c.477-1G>A

Other names:

GLRA1

HGVS:

NC_000005.10:g.151856384C>T
NG_011764.1:g.73453G>A
NM_000171.4:c.477-1G>AMANE SELECT
NM_001146040.2:c.477-1G>A
NM_001292000.2:c.228-1G>A
NC_000005.9:g.151235945C>T

Links:

dbSNP: rs762864856

NCBI 1000 Genomes Browser:

rs762864856

Molecular consequence:

NM_000171.4:c.477-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001146040.2:c.477-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001292000.2:c.228-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]

Functional consequence:

cryptic splice acceptor activation [Variation Ontology: 0375]

Observations:

Condition(s)

Name:: Hyperekplexia 1 (STHE)
Synonyms:: Startle disease, familial; Startle reaction, exaggerated; Stiff-baby syndrome; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0007868; MedGen: C4551954; Orphanet: 3197; OMIM: 149400

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000612167	Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic	inherited	clinical testing	PubMed (2) [See all records that cite these PMIDs] 25741868, 28879899

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000612167

Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic

inherited

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
Indian	inherited	yes	1	not provided	not provided	not provided	not provided	clinical testing

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

Hyperekplexia: A forgotten diagnosis clinched by next-generation sequencing.

Lallar M, Srivastava A, Phadke SR.

Neurol India. 2017 Sep-Oct;65(5):1065-1067. doi: 10.4103/neuroindia.NI_851_16.

PubMed [citation]

PMID:: 28879899

Details of each submission

From Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, SCV000612167.1

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

Description

A homozygous 3â€™ splice site variation in the GLRA1 gene (chr5:151235945; C>T) that affects the invariant CT acceptor splice site of exon 5 (c.477-1G>A; ENST00000455880) was detected. This 3â€™ splice variation is considered pathogenic because it is not present in the 1000 Genomes database and has a minor allele frequency of less than 0.001% in the ExAC database. It is predicted to be damaging by the pathogenicity predication software such as MutationTaster and Human Splicing Finder. This region is conserved across species.

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

Last Updated: Jun 23, 2024

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