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NM_004287.5(GOSR2):c.104A>G (p.Asn35Ser) AND Progressive myoclonic epilepsy

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Nov 15, 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:
RCV002536324.3

Allele description [Variation Report for NM_004287.5(GOSR2):c.104A>G (p.Asn35Ser)]

NM_004287.5(GOSR2):c.104A>G (p.Asn35Ser)

Genes:
LOC126862578:BRD4-independent group 4 enhancer GRCh37_chr17:45008344-45009543 [Gene]
GOSR2:golgi SNAP receptor complex member 2 [Gene - OMIM - HGNC]
LRRC37A2:leucine rich repeat containing 37 member A2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17q21.32
Genomic location:
Preferred name:
NM_004287.5(GOSR2):c.104A>G (p.Asn35Ser)
HGVS:
  • NC_000017.11:g.46931108A>G
  • NG_031806.2:g.12989A>G
  • NM_001012511.3:c.104A>G
  • NM_001321133.2:c.104A>G
  • NM_001321134.2:c.50A>G
  • NM_001330252.2:c.104A>G
  • NM_001353114.2:c.101A>G
  • NM_001353115.2:c.101A>G
  • NM_001353116.2:c.101A>G
  • NM_001363851.2:c.50A>G
  • NM_004287.5:c.104A>GMANE SELECT
  • NM_054022.4:c.104A>G
  • NP_001012529.1:p.Asn35Ser
  • NP_001308062.1:p.Asn35Ser
  • NP_001308063.1:p.Asn17Ser
  • NP_001317181.1:p.Asn35Ser
  • NP_001340043.1:p.Asn34Ser
  • NP_001340044.1:p.Asn34Ser
  • NP_001340045.1:p.Asn34Ser
  • NP_001350780.1:p.Asn17Ser
  • NP_004278.2:p.Asn35Ser
  • NP_473363.1:p.Asn35Ser
  • NC_000017.10:g.45008474A>G
  • NM_004287.3:c.104A>G
  • NR_148349.2:n.137A>G
  • NR_148350.2:n.137A>G
  • NR_148351.2:n.137A>G
Protein change:
N17S
Links:
dbSNP: rs148962223
NCBI 1000 Genomes Browser:
rs148962223
Molecular consequence:
  • NM_001012511.3:c.104A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001321133.2:c.104A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001321134.2:c.50A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330252.2:c.104A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353114.2:c.101A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353115.2:c.101A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353116.2:c.101A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001363851.2:c.50A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004287.5:c.104A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_054022.4:c.104A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NR_148349.2:n.137A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148350.2:n.137A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148351.2:n.137A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Progressive myoclonic epilepsy
Synonyms:
Myoclonic Epilepsies, Progressive; Familial progressive myoclonic epilepsy; Progressive myoclonus epilepsy; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0020074; MedGen: C0751778; Orphanet: 308; OMIM: PS254800

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003005533Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Nov 15, 2022) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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, SCV003005533.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

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. ClinVar contains an entry for this variant (Variation ID: 546434). This variant has not been reported in the literature in individuals affected with GOSR2-related conditions. This variant is present in population databases (rs148962223, gnomAD 0.002%). This sequence change replaces asparagine, which is neutral and polar, with serine, which is neutral and polar, at codon 35 of the GOSR2 protein (p.Asn35Ser).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024