NM_014141.6(CNTNAP2):c.1078A>G (p.Asn360Asp) AND Cortical dysplasia-focal epilepsy syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 27, 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:: RCV000232850.7

Allele description [Variation Report for NM_014141.6(CNTNAP2):c.1078A>G (p.Asn360Asp)]

NM_014141.6(CNTNAP2):c.1078A>G (p.Asn360Asp)

Gene:

CNTNAP2:contactin associated protein 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7q35

Genomic location:

Preferred name:

NM_014141.6(CNTNAP2):c.1078A>G (p.Asn360Asp)

Other names:

p.N360D:AAT>GAT

HGVS:

NC_000007.14:g.147128831A>G
NG_007092.3:g.1017831A>G
NM_014141.6:c.1078A>GMANE SELECT
NP_054860.1:p.Asn360Asp
NC_000007.13:g.146825923A>G
NG_007092.2:g.1017471A>G
NM_014141.4:c.1078A>G
NM_014141.5:c.1078A>G

Protein change:

N360D

Links:

dbSNP: rs570190374

NCBI 1000 Genomes Browser:

rs570190374

Molecular consequence:

NM_014141.6:c.1078A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Cortical dysplasia-focal epilepsy syndrome (PTHSL1)
Synonyms:: Pitt-Hopkins-like syndrome 1
Identifiers:: MONDO: MONDO:0012400; MedGen: C2750246; Orphanet: 221150; OMIM: 610042

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Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000289923	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 27, 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

SCV000289923

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 27, 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, SCV000289923.5

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

Description

This sequence change replaces asparagine, which is neutral and polar, with aspartic acid, which is acidic and polar, at codon 360 of the CNTNAP2 protein (p.Asn360Asp). This variant is present in population databases (rs570190374, gnomAD 0.2%). This variant has not been reported in the literature in individuals affected with CNTNAP2-related conditions. ClinVar contains an entry for this variant (Variation ID: 205230). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The aspartic acid amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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.

#	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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