U.S. flag

An official website of the United States government

NM_001330078.2(NRXN1):c.3752G>C (p.Arg1251Thr) AND Pitt-Hopkins-like syndrome 2

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Nov 6, 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:
RCV003510429.1

Allele description

NM_001330078.2(NRXN1):c.3752G>C (p.Arg1251Thr)

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.3752G>C (p.Arg1251Thr)
HGVS:
  • NC_000002.12:g.50055011C>G
  • NG_011878.1:g.982526G>C
  • NM_001135659.3:c.3872G>C
  • NM_001330077.2:c.3728G>C
  • NM_001330078.2:c.3752G>CMANE SELECT
  • NM_001330082.2:c.3728G>C
  • NM_001330083.2:c.3653-1421G>C
  • NM_001330084.2:c.3686G>C
  • NM_001330085.2:c.3725G>C
  • NM_001330086.2:c.3752G>C
  • NM_001330087.2:c.3608-1421G>C
  • NM_001330088.2:c.3638-1421G>C
  • NM_001330091.2:c.647G>C
  • NM_001330092.2:c.647G>C
  • NM_001330093.2:c.3749G>C
  • NM_001330094.2:c.3740G>C
  • NM_001330095.2:c.3668-1421G>C
  • NM_001330096.2:c.3608-1421G>C
  • NM_001330097.2:c.614-1421G>C
  • NM_004801.6:c.3719-1421G>C
  • NM_138735.5:c.614-1421G>C
  • NP_001129131.1:p.Arg1291Thr
  • NP_001317006.1:p.Arg1243Thr
  • NP_001317007.1:p.Arg1251Thr
  • NP_001317011.1:p.Arg1243Thr
  • NP_001317013.1:p.Arg1229Thr
  • NP_001317014.1:p.Arg1242Thr
  • NP_001317015.1:p.Arg1251Thr
  • NP_001317020.1:p.Arg216Thr
  • NP_001317021.1:p.Arg216Thr
  • NP_001317022.1:p.Arg1250Thr
  • NP_001317023.1:p.Arg1247Thr
  • NC_000002.11:g.50282149C>G
Protein change:
R1229T
Molecular consequence:
  • NM_001330083.2:c.3653-1421G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001330087.2:c.3608-1421G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001330088.2:c.3638-1421G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001330095.2:c.3668-1421G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001330096.2:c.3608-1421G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001330097.2:c.614-1421G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_004801.6:c.3719-1421G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_138735.5:c.614-1421G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001135659.3:c.3872G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330077.2:c.3728G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330078.2:c.3752G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330082.2:c.3728G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330084.2:c.3686G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330085.2:c.3725G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330086.2:c.3752G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330091.2:c.647G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330092.2:c.647G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330093.2:c.3749G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330094.2:c.3740G>C - 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

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004336161Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Nov 6, 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 Invitae, SCV004336161.1

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

Description

This sequence change replaces arginine, which is basic and polar, with threonine, which is neutral and polar, at codon 1291 of the NRXN1 protein (p.Arg1291Thr). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with NRXN1-related conditions. 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: Feb 20, 2024