NM_000171.4(GLRA1):c.1139_1162del (p.Ile380_Asn387del) AND Hereditary hyperekplexia

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 10, 2022
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:: RCV002982351.3

Allele description [Variation Report for NM_000171.4(GLRA1):c.1139_1162del (p.Ile380_Asn387del)]

NM_000171.4(GLRA1):c.1139_1162del (p.Ile380_Asn387del)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

5q33.1

Genomic location:

Preferred name:

NM_000171.4(GLRA1):c.1139_1162del (p.Ile380_Asn387del)

HGVS:

NC_000005.10:g.151822863_151822886del
NG_011764.1:g.106953_106976del
NM_000171.4:c.1139_1162delMANE SELECT
NM_001146040.2:c.1163_1186del
NM_001292000.2:c.890_913del
NP_000162.2:p.Ile380_Asn387del
NP_001139512.1:p.Ile388_Asn395del
NP_001278929.1:p.Ile297_Asn304del
NC_000005.9:g.151202422_151202445del
NC_000005.9:g.151202424_151202447del

Molecular consequence:

NM_000171.4:c.1139_1162del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001146040.2:c.1163_1186del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001292000.2:c.890_913del - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Name:: Hereditary hyperekplexia
Synonyms:: Hyperexplexia, hereditary
Identifiers:: MONDO: MONDO:0021022; MedGen: C1835614; OMIM: PS149400

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LOC4334821 [Oryza sativa Japonica Group]
LOC4334821 [Oryza sativa Japonica Group]
Gene ID:4334821

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003288202	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 10, 2022)	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

SCV003288202

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 10, 2022)

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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003288202.2

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

Description

This variant is not present in population databases (gnomAD no frequency). 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. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has not been reported in the literature in individuals affected with GLRA1-related conditions. This variant, c.1139_1162del, results in the deletion of 8 amino acid(s) of the GLRA1 protein (p.Ile380_Asn387del), but otherwise preserves the integrity of the reading frame.

#	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: Sep 29, 2024

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