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NM_014141.6(CNTNAP2):c.1007G>T (p.Cys336Phe) AND Cortical dysplasia-focal epilepsy syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jul 14, 2023
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:
RCV001940657.6

Allele description [Variation Report for NM_014141.6(CNTNAP2):c.1007G>T (p.Cys336Phe)]

NM_014141.6(CNTNAP2):c.1007G>T (p.Cys336Phe)

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.1007G>T (p.Cys336Phe)
HGVS:
  • NC_000007.14:g.147128760G>T
  • NG_007092.3:g.1017760G>T
  • NM_014141.6:c.1007G>TMANE SELECT
  • NP_054860.1:p.Cys336Phe
  • NC_000007.13:g.146825852G>T
Protein change:
C336F
Links:
dbSNP: rs1229878290
NCBI 1000 Genomes Browser:
rs1229878290
Molecular consequence:
  • NM_014141.6:c.1007G>T - 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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002195845Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jul 14, 2023) 		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, SCV002195845.3

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

Description

This sequence change replaces cysteine, which is neutral and slightly polar, with phenylalanine, which is neutral and non-polar, at codon 336 of the CNTNAP2 protein (p.Cys336Phe). This variant is not present in population databases (gnomAD no frequency). 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: 1419438). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. 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.

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

Last Updated: Sep 29, 2024