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NM_001330078.2(NRXN1):c.772+1105T>A AND Pitt-Hopkins-like syndrome 2

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 16, 2020
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:
RCV001347892.7

Allele description [Variation Report for NM_001330078.2(NRXN1):c.772+1105T>A]

NM_001330078.2(NRXN1):c.772+1105T>A

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.772+1105T>A
HGVS:
  • NC_000002.12:g.51026397A>T
  • NG_011878.1:g.11140T>A
  • NM_001135659.3:c.845T>A
  • NM_001330077.2:c.772+1105T>A
  • NM_001330078.2:c.772+1105T>AMANE SELECT
  • NM_001330079.2:c.772+1105T>A
  • NM_001330081.2:c.772+1105T>A
  • NM_001330082.2:c.772+1105T>A
  • NM_001330083.2:c.772+1105T>A
  • NM_001330084.2:c.772+1105T>A
  • NM_001330085.2:c.772+1105T>A
  • NM_001330086.2:c.772+1105T>A
  • NM_001330087.2:c.772+1105T>A
  • NM_001330088.2:c.772+1105T>A
  • NM_001330089.2:c.772+1105T>A
  • NM_001330090.2:c.772+1105T>A
  • NM_001330093.2:c.772+1105T>A
  • NM_001330094.2:c.772+1105T>A
  • NM_001330095.2:c.772+1105T>A
  • NM_001330096.2:c.772+1105T>A
  • NM_004801.6:c.772+1105T>A
  • NP_001129131.1:p.Ile282Lys
  • NC_000002.11:g.51253535A>T
Protein change:
I282K
Links:
dbSNP: rs1670475413
NCBI 1000 Genomes Browser:
rs1670475413
Molecular consequence:
  • NM_001330077.2:c.772+1105T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001330078.2:c.772+1105T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001330079.2:c.772+1105T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001330081.2:c.772+1105T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001330082.2:c.772+1105T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001330083.2:c.772+1105T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001330084.2:c.772+1105T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001330085.2:c.772+1105T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001330086.2:c.772+1105T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001330087.2:c.772+1105T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001330088.2:c.772+1105T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001330089.2:c.772+1105T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001330090.2:c.772+1105T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001330093.2:c.772+1105T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001330094.2:c.772+1105T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001330095.2:c.772+1105T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001330096.2:c.772+1105T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_004801.6:c.772+1105T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001135659.3:c.845T>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001542173Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Sep 16, 2020) 		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, SCV001542173.4

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

Description

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 missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals with NRXN1-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces isoleucine with lysine at codon 282 of the NRXN1 protein (p.Ile282Lys). The isoleucine residue is weakly conserved and there is a moderate physicochemical difference between isoleucine and lysine.

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

Last Updated: Sep 29, 2024