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NM_001099922.3(ALG13):c.320A>G (p.Asn107Ser) AND Inborn genetic diseases

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 30, 2017
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:
RCV002321552.4

Allele description [Variation Report for NM_001099922.3(ALG13):c.320A>G (p.Asn107Ser)]

NM_001099922.3(ALG13):c.320A>G (p.Asn107Ser)

Gene:
ALG13:ALG13 UDP-N-acetylglucosaminyltransferase subunit [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xq23
Genomic location:
Preferred name:
NM_001099922.3(ALG13):c.320A>G (p.Asn107Ser)
HGVS:
  • NC_000023.11:g.111685040A>G
  • NG_016238.1:g.8923A>G
  • NM_001039210.5:c.261A>G
  • NM_001099922.3:c.320A>GMANE SELECT
  • NM_001168385.3:c.320A>G
  • NM_001257230.2:c.8A>G
  • NM_001257231.2:c.86A>G
  • NM_001257234.2:c.8A>G
  • NM_001257235.3:c.8A>G
  • NM_001257237.2:c.8A>G
  • NM_001257239.3:c.8A>G
  • NM_001257240.3:c.8A>G
  • NM_001257241.3:c.86A>G
  • NM_001324290.2:c.326A>G
  • NM_001324291.2:c.8A>G
  • NM_001324292.2:c.320A>G
  • NM_001324293.1:c.8A>G
  • NM_001324294.2:c.8A>G
  • NM_018466.6:c.320A>G
  • NP_001034299.3:p.Gln87=
  • NP_001093392.1:p.Asn107Ser
  • NP_001161857.1:p.Asn107Ser
  • NP_001244159.1:p.Asn3Ser
  • NP_001244160.1:p.Asn29Ser
  • NP_001244160.1:p.Asn29Ser
  • NP_001244163.1:p.Asn3Ser
  • NP_001244164.1:p.Asn3Ser
  • NP_001244166.1:p.Asn3Ser
  • NP_001244168.1:p.Asn3Ser
  • NP_001244169.1:p.Asn3Ser
  • NP_001244170.1:p.Asn29Ser
  • NP_001311219.1:p.Asn109Ser
  • NP_001311220.1:p.Asn3Ser
  • NP_001311221.1:p.Asn107Ser
  • NP_001311222.1:p.Asn3Ser
  • NP_001311223.1:p.Asn3Ser
  • NP_060936.1:p.Asn107Ser
  • NC_000023.10:g.110928268A>G
  • NM_001099922.2:c.320A>G
  • NM_001099922.2:c.[320A>G]
  • NM_001099922.3:c.320A>G
  • NM_001257230.1:c.8A>G
  • NM_001257231.1:c.86A>G
  • NM_001257235.1:c.8A>G
  • NR_033125.3:n.265A>G
  • NR_136735.2:n.390A>G
  • NR_148693.2:n.369A>G
  • p.N107S
Protein change:
N107S; ASN107SER
Links:
OMIM: 300776.0002; dbSNP: rs398122394
NCBI 1000 Genomes Browser:
rs398122394
Molecular consequence:
  • NM_001099922.3:c.320A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001168385.3:c.320A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001257230.2:c.8A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001257231.2:c.86A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001257234.2:c.8A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001257235.3:c.8A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001257237.2:c.8A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001257239.3:c.8A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001257240.3:c.8A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001257241.3:c.86A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001324290.2:c.326A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001324291.2:c.8A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001324292.2:c.320A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001324293.1:c.8A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001324294.2:c.8A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_018466.6:c.320A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NR_033125.3:n.265A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_136735.2:n.390A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148693.2:n.369A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001039210.5:c.261A>G - synonymous variant - [Sequence Ontology: SO:0001819]

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
SCV002610690Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Pathogenic
(Oct 30, 2017) 		germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Citation Link

Help

Summary from all submissions

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

Citations

PubMed

Diagnostic exome sequencing in persons with severe intellectual disability.

de Ligt J, Willemsen MH, van Bon BW, Kleefstra T, Yntema HG, Kroes T, Vulto-van Silfhout AT, Koolen DA, de Vries P, Gilissen C, del Rosario M, Hoischen A, Scheffer H, de Vries BB, Brunner HG, Veltman JA, Vissers LE.

N Engl J Med. 2012 Nov 15;367(20):1921-9. doi: 10.1056/NEJMoa1206524. Epub 2012 Oct 3.

PubMed [citation]
PMID:
23033978

De novo mutations in epileptic encephalopathies.

Epi4K Consortium; Epilepsy Phenome/Genome Project, Allen AS, Berkovic SF, Cossette P, Delanty N, Dlugos D, Eichler EE, Epstein MP, Glauser T, Goldstein DB, Han Y, Heinzen EL, Hitomi Y, Howell KB, Johnson MR, Kuzniecky R, Lowenstein DH, Lu YF, Madou MR, Marson AG, Mefford HC, et al.

Nature. 2013 Sep 12;501(7466):217-21. doi: 10.1038/nature12439. Epub 2013 Aug 11.

PubMed [citation]
PMID:
23934111
PMCID:
PMC3773011
See all PubMed Citations (5)

Details of each submission

From Ambry Genetics, SCV002610690.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

The p.N107S pathogenic mutation (also known as c.320A>G), located in coding exon 3 of the ALG13 gene, results from an A to G substitution at nucleotide position 320. The asparagine at codon 107 is replaced by serine, an amino acid with highly similar properties. This mutation has been detected as a de novo occurrence in several individuals with early onset epileptic encephalopathy, infantile spasms, and severe intellectual disability (de Ligt J et al. N. Engl. J. Med., 2012 Nov;367:1921-9; Allen et al. Nature, 2013 Sep;501:217-21; Michaud JL et al. Hum. Mol. Genet., 2014 Sep;23:4846-58; Dimassi S et al. Clin. Genet., 2016 Feb;89:198-204). In one female patient, X-inactivation studies demonstrated a random pattern of X-inactivation, with no evidence of skewness (Hamici S et al. Eur J Med Genet, 2017 Oct;60:541-547). Based on the supporting evidence, p.N107S is interpreted as a disease-causing mutation.

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

Last Updated: Nov 24, 2024