NM_144573.3(NEXN):c.65A>G (p.Tyr22Cys) AND not specified

Clinical significance:Uncertain significance (Last evaluated: Dec 2, 2016)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000414636.1

Allele description [Variation Report for NM_144573.3(NEXN):c.65A>G (p.Tyr22Cys)]

NM_144573.3(NEXN):c.65A>G (p.Tyr22Cys)

Gene:
NEXN:nexilin F-actin binding protein [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p31.1
Genomic location:
Preferred name:
NM_144573.3(NEXN):c.65A>G (p.Tyr22Cys)
HGVS:
  • NC_000001.11:g.77917603A>G
  • NG_016625.1:g.34089A>G
  • NM_001172309.1:c.28-357A>G
  • NM_144573.3:c.65A>G
  • NP_653174.3:p.Tyr22Cys
  • LRG_442t1:c.65A>G
  • LRG_442:g.34089A>G
  • LRG_442p1:p.Tyr22Cys
  • NC_000001.10:g.78383288A>G
Protein change:
Y22C
Links:
dbSNP: rs1057518512
NCBI 1000 Genomes Browser:
rs1057518512
Molecular consequence:
  • NM_001172309.1:c.28-357A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_144573.3:c.65A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000492238GeneDxcriteria provided, single submitter
Uncertain significance
(Dec 2, 2016)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000492238.1

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

Description

A novel variant of uncertain significance has been identified in the NEXN gene. The Y22C variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. It was not observed in approximately 6,000 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. In addition, the Y22C variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. Moreover, this substitution occurs at a position that is conserved across species, and in silico analysis predicts this variant is probably damaging to the protein structure/function. Nonetheless, this variant lacks observation in a significant number of affected individuals, segregation data, and functional evidence, all of which would further clarify pathogenicity.Therefore, based on the currently available information, it is unclear whether this variant is pathogenic or rare benign. This result cannot be interpreted for diagnosis or used for family member screening at this time.

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

Last Updated: Feb 27, 2021

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