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NM_022041.4(GAN):c.973G>A (p.Glu325Lys) AND Inborn genetic diseases

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 2, 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:
RCV002370063.2

Allele description [Variation Report for NM_022041.4(GAN):c.973G>A (p.Glu325Lys)]

NM_022041.4(GAN):c.973G>A (p.Glu325Lys)

Gene:
GAN:gigaxonin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16q23.2
Genomic location:
Preferred name:
NM_022041.4(GAN):c.973G>A (p.Glu325Lys)
HGVS:
  • NC_000016.10:g.81357931G>A
  • NG_009007.1:g.47966G>A
  • NM_001377486.1:c.334G>A
  • NM_022041.4:c.973G>AMANE SELECT
  • NP_001364415.1:p.Glu112Lys
  • NP_071324.1:p.Glu325Lys
  • NP_071324.1:p.Glu325Lys
  • LRG_242t1:c.973G>A
  • LRG_242:g.47966G>A
  • LRG_242p1:p.Glu325Lys
  • NC_000016.9:g.81391536G>A
  • NM_022041.3:c.973G>A
Protein change:
E112K
Links:
dbSNP: rs1597403411
NCBI 1000 Genomes Browser:
rs1597403411
Molecular consequence:
  • NM_001377486.1:c.334G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_022041.4:c.973G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Inborn genetic diseases
Identifiers:
MeSH: D030342; MedGen: C0950123

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002692754Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Uncertain significance
(Sep 2, 2020) 		germlineclinical testing

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

Citation Link

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Summary from all submissions

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

Citations

PubMed

A novel mutation in the GAN gene causes an intermediate form of giant axonal neuropathy in an Arab-Israeli family.

Abu-Rashid M, Mahajnah M, Jaber L, Kornreich L, Bar-On E, Basel-Vanagaite L, Soffer D, Koenig M, Straussberg R.

Eur J Paediatr Neurol. 2013 May;17(3):259-64. doi: 10.1016/j.ejpn.2012.10.012. Epub 2013 Jan 16.

PubMed [citation]
PMID:
23332420

Details of each submission

From Ambry Genetics, SCV002692754.2

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

Description

The c.973G>A variant (also known as p.E325K), located in coding exon 5 of the GAN gene, results from a G to A substitution at nucleotide position 973. The glutamic acid at codon 325 is replaced by lysine, an amino acid with similar properties. However, this change occurs in the last base pair of coding exon 5, which makes it likely to have some effect on normal mRNA splicing. This alteration has been reported, in a presumed homozygous state, in two related consanguineous families in four children who presented with a clinical phenotype of giant axonal neuropathy (Abu-Rashid M et al. Eur. J. Paediatr. Neurol., 2013 May;17:259-64). This nucleotide position is highly conserved in available vertebrate species. This amino acid position is well conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice donor site. In addition, as a missense substitution this is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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

Last Updated: May 1, 2024