NM_014141.6(CNTNAP2):c.1247C>T (p.Ala416Val) AND not specified

Germline classification:: Benign/Likely benign (4 submissions)
Last evaluated:: May 5, 2017
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000116772.23

Allele description [Variation Report for NM_014141.6(CNTNAP2):c.1247C>T (p.Ala416Val)]

NM_014141.6(CNTNAP2):c.1247C>T (p.Ala416Val)

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.1247C>T (p.Ala416Val)

Other names:

p.A416V:GCG>GTG

HGVS:

NC_000007.14:g.147132408C>T
NG_007092.3:g.1021408C>T
NM_014141.6:c.1247C>TMANE SELECT
NP_054860.1:p.Ala416Val
NC_000007.13:g.146829500C>T
NG_007092.2:g.1021048C>T
NM_014141.4:c.1247C>T
NM_014141.5:c.1247C>T

Protein change:

A416V

Links:

dbSNP: rs34456867

NCBI 1000 Genomes Browser:

rs34456867

Molecular consequence:

NM_014141.6:c.1247C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000150748	Genetic Services Laboratory, University of Chicago	no assertion criteria provided	Likely benign	germline	clinical testing
SCV000167790	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Benign (Jan 16, 2013)	germline	clinical testing	Citation Link,
SCV000312062	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000612855	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Likely benign (May 5, 2017)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 24807205, 25621974, 26467025

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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	germline	yes	not provided	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

A study of the role of the FOXP2 and CNTNAP2 genes in persistent developmental stuttering.

Han TU, Park J, Domingues CF, Moretti-Ferreira D, Paris E, Sainz E, Gutierrez J, Drayna D.

Neurobiol Dis. 2014 Sep;69:23-31. doi: 10.1016/j.nbd.2014.04.019. Epub 2014 May 5.

PubMed [citation]

PMID:: 24807205
PMCID:: PMC4099264

See all PubMed Citations (4)

Details of each submission

From Genetic Services Laboratory, University of Chicago, SCV000150748.2

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

Description

Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed.

#	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

From GeneDx, SCV000167790.12

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

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From PreventionGenetics, part of Exact Sciences, SCV000312062.1

#	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

From Athena Diagnostics, SCV000612855.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

#	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: Nov 3, 2024

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