NM_001330078.2(NRXN1):c.3718+8A>G AND Pitt-Hopkins-like syndrome 2

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 8, 2018
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:: RCV000818765.6

Allele description [Variation Report for NM_001330078.2(NRXN1):c.3718+8A>G]

NM_001330078.2(NRXN1):c.3718+8A>G

Gene:

NRXN1:neurexin 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2p16.3

Genomic location:

Preferred name:

NM_001330078.2(NRXN1):c.3718+8A>G

HGVS:

NC_000002.12:g.50091315T>C
NG_011878.1:g.946222A>G
NM_001135659.3:c.3838+8A>G
NM_001330077.2:c.3694+8A>G
NM_001330078.2:c.3718+8A>GMANE SELECT
NM_001330082.2:c.3694+8A>G
NM_001330083.2:c.3652+8A>G
NM_001330084.2:c.3652+8A>G
NM_001330085.2:c.3691+8A>G
NM_001330086.2:c.3718+8A>G
NM_001330087.2:c.3607+8A>G
NM_001330088.2:c.3637+8A>G
NM_001330091.2:c.613+8A>G
NM_001330092.2:c.613+8A>G
NM_001330093.2:c.3715+8A>G
NM_001330094.2:c.3706+8A>G
NM_001330095.2:c.3667+8A>G
NM_001330096.2:c.3607+8A>G
NM_001330097.2:c.613+8A>G
NM_004801.6:c.3718+8A>G
NM_138735.5:c.613+8A>G
NC_000002.11:g.50318453T>C
NM_001135659.1:c.3838+8A>G

Links:

dbSNP: rs939526667

NCBI 1000 Genomes Browser:

rs939526667

Molecular consequence:

NM_001135659.3:c.3838+8A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001330077.2:c.3694+8A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001330078.2:c.3718+8A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001330082.2:c.3694+8A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001330083.2:c.3652+8A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001330084.2:c.3652+8A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001330085.2:c.3691+8A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001330086.2:c.3718+8A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001330087.2:c.3607+8A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001330088.2:c.3637+8A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001330091.2:c.613+8A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001330092.2:c.613+8A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001330093.2:c.3715+8A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001330094.2:c.3706+8A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001330095.2:c.3667+8A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001330096.2:c.3607+8A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001330097.2:c.613+8A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_004801.6:c.3718+8A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_138735.5:c.613+8A>G - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Pitt-Hopkins-like syndrome 2 (PTHSL2)
Identifiers:: MONDO: MONDO:0013690; MedGen: C3280479; Orphanet: 221150; OMIM: 614325

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000959396	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 8, 2018)	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

SCV000959396

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 8, 2018)

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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV000959396.4

#	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 falls in intron 20 of the NRXN1 gene. It does not directly change the encoded amino acid sequence of the NRXN1 protein. 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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. This variant has not been reported in the literature in individuals with NRXN1-related disease. This variant is not present in population databases (ExAC no frequency).

#	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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