NM_001330078.2(NRXN1):c.3090A>C (p.Gly1030=) AND not specified

Clinical significance:Benign/Likely benign (Last evaluated: Jan 8, 2016)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:

Allele description [Variation Report for NM_001330078.2(NRXN1):c.3090A>C (p.Gly1030=)]

NM_001330078.2(NRXN1):c.3090A>C (p.Gly1030=)

NRXN1:neurexin 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_001330078.2(NRXN1):c.3090A>C (p.Gly1030=)
Other names:
  • NC_000002.12:g.50472452T>G
  • NG_011878.1:g.565085A>C
  • NM_001135659.2:c.3210A>C
  • NM_001330077.1:c.3066A>C
  • NM_001330078.2:c.3090A>CMANE SELECT
  • NM_001330082.1:c.3066A>C
  • NM_001330083.1:c.3024A>C
  • NM_001330084.1:c.3024A>C
  • NM_001330085.1:c.3063A>C
  • NM_001330086.1:c.3090A>C
  • NM_001330087.1:c.2979A>C
  • NM_001330088.1:c.3009A>C
  • NM_001330093.1:c.3087A>C
  • NM_001330094.1:c.3078A>C
  • NM_001330095.1:c.3039A>C
  • NM_001330096.1:c.2979A>C
  • NM_004801.5:c.3090A>C
  • NP_001129131.1:p.Gly1070=
  • NP_001317006.1:p.Gly1022=
  • NP_001317007.1:p.Gly1030=
  • NP_001317011.1:p.Gly1022=
  • NP_001317012.1:p.Gly1008=
  • NP_001317013.1:p.Gly1008=
  • NP_001317014.1:p.Gly1021=
  • NP_001317015.1:p.Gly1030=
  • NP_001317016.1:p.Gly993=
  • NP_001317017.1:p.Gly1003=
  • NP_001317022.1:p.Gly1029=
  • NP_001317023.1:p.Gly1026=
  • NP_001317024.1:p.Gly1013=
  • NP_001317025.1:p.Gly993=
  • NP_004792.1:p.Gly1030=
  • NC_000002.11:g.50699590T>G
  • NM_001135659.1:c.3210A>C
dbSNP: rs201886024
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_001135659.2:c.3210A>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001330077.1:c.3066A>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001330078.2:c.3090A>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001330082.1:c.3066A>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001330083.1:c.3024A>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001330084.1:c.3024A>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001330085.1:c.3063A>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001330086.1:c.3090A>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001330087.1:c.2979A>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001330088.1:c.3009A>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001330093.1:c.3087A>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001330094.1:c.3078A>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001330095.1:c.3039A>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001330096.1:c.2979A>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_004801.5:c.3090A>C - synonymous variant - [Sequence Ontology: SO:0001819]


MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000241844GeneDxcriteria provided, single submitter
(Oct 6, 2014)
germlineclinical testing

Citation Link,

SCV000596065Genetic Services Laboratory, University of Chicagocriteria provided, single submitter
Likely benign
(Jan 8, 2016)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenonot providednot providednot providednot providednot providedclinical testing
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing



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]

Details of each submission

From GeneDx, SCV000241844.11

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided


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.

OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Genetic Services Laboratory, University of Chicago, SCV000596065.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenonot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 27, 2021

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