NM_005076.5(CNTN2):c.1075C>A (p.Arg359Ser) AND Epilepsy, familial adult myoclonic, 5

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Jan 19, 2024
Review status:: criteria provided, conflicting classifications

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:: RCV000625909.13

Allele description [Variation Report for NM_005076.5(CNTN2):c.1075C>A (p.Arg359Ser)]

NM_005076.5(CNTN2):c.1075C>A (p.Arg359Ser)

Gene:

CNTN2:contactin 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1q32.1

Genomic location:

Preferred name:

NM_005076.5(CNTN2):c.1075C>A (p.Arg359Ser)

HGVS:

NC_000001.11:g.205061966C>A
NG_033845.1:g.23755C>A
NM_001346083.2:c.1075C>A
NM_005076.5:c.1075C>AMANE SELECT
NP_001333012.1:p.Arg359Ser
NP_005067.1:p.Arg359Ser
NC_000001.10:g.205031094C>A
NM_005076.3:c.1075C>A
NM_005076.4:c.1075C>A
NR_144350.2:n.1344C>A

Protein change:

R359S

Links:

dbSNP: rs371816961

NCBI 1000 Genomes Browser:

rs371816961

Molecular consequence:

NM_001346083.2:c.1075C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_005076.5:c.1075C>A - missense variant - [Sequence Ontology: SO:0001583]
NR_144350.2:n.1344C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Name:: Epilepsy, familial adult myoclonic, 5 (FAME5)
Synonyms:: CORTICAL MYOCLONIC TREMOR WITH EPILEPSY, FAMILIAL, 5
Identifiers:: MONDO: MONDO:0014167; MedGen: C3809374; Orphanet: 86814; OMIM: 615400

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000746491	Genomic Research Center, Shahid Beheshti University of Medical Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Apr 6, 2019)	inherited	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001072735	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jan 19, 2024)	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

SCV000746491

Genomic Research Center, Shahid Beheshti University of Medical Sciences

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Apr 6, 2019)

inherited

clinical testing

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

SCV001072735

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Jan 19, 2024)

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
not provided	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

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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Genomic Research Center, Shahid Beheshti University of Medical Sciences, SCV000746491.2

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

From Invitae, SCV001072735.6

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

Last Updated: Feb 20, 2024

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