NM_014141.6(CNTNAP2):c.3716-2A>G AND Cortical dysplasia-focal epilepsy syndrome

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jan 2, 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:: RCV001989682.4

Allele description [Variation Report for NM_014141.6(CNTNAP2):c.3716-2A>G]

NM_014141.6(CNTNAP2):c.3716-2A>G

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

7q36.1

Genomic location:

Preferred name:

NM_014141.6(CNTNAP2):c.3716-2A>G

HGVS:

NC_000007.14:g.148409389A>G
NG_007092.3:g.2298389A>G
NM_014141.6:c.3716-2A>GMANE SELECT
NC_000007.13:g.148106481A>G

Links:

dbSNP: rs746894028

NCBI 1000 Genomes Browser:

rs746894028

Molecular consequence:

NM_014141.6:c.3716-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002282978	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely pathogenic (Jan 2, 2023)	germline	clinical testing	PubMed (7) [See all records that cite these PMIDs] 16199547, 19896112, 21827697, 25045150, 26843181, 27439707, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002282978

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely pathogenic
(Jan 2, 2023)

germline

clinical testing

PubMed (7)
[See all records that cite these PMIDs]

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

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]

PMID:: 16199547
PMCID:: PMC1735933

CNTNAP2 and NRXN1 are mutated in autosomal-recessive Pitt-Hopkins-like mental retardation and determine the level of a common synaptic protein in Drosophila.

Zweier C, de Jong EK, Zweier M, Orrico A, Ousager LB, Collins AL, Bijlsma EK, Oortveld MA, Ekici AB, Reis A, Schenck A, Rauch A.

Am J Hum Genet. 2009 Nov;85(5):655-66. doi: 10.1016/j.ajhg.2009.10.004. Epub 2009 Nov 5.

PubMed [citation]

PMID:: 19896112
PMCID:: PMC2775834

See all PubMed Citations (7)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002282978.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (7)

Description

In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 1494963). This variant has not been reported in the literature in individuals affected with CNTNAP2-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This sequence change affects an acceptor splice site in intron 22 of the CNTNAP2 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in CNTNAP2 are known to be pathogenic (PMID: 19896112, 21827697, 25045150, 26843181, 27439707).

#	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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