NM_000401.3(EXT2):c.110C>T (p.Ser37Leu) AND Seizures, scoliosis, and macrocephaly syndrome

Clinical significance:Likely pathogenic (Last evaluated: Jul 7, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000663343.3

Allele description [Variation Report for NM_000401.3(EXT2):c.110C>T (p.Ser37Leu)]

NM_000401.3(EXT2):c.110C>T (p.Ser37Leu)

Gene:
EXT2:exostosin glycosyltransferase 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11p11.2
Genomic location:
Preferred name:
NM_000401.3(EXT2):c.110C>T (p.Ser37Leu)
HGVS:
  • NC_000011.10:g.44107723C>T
  • NG_007560.1:g.17175C>T
  • NM_000401.3:c.110C>T
  • NM_001178083.2:c.11C>T
  • NM_207122.1:c.11C>T
  • NP_000392.3:p.Ser37Leu
  • NP_001171554.1:p.Ser4Leu
  • NP_997005.1:p.Ser4Leu
  • LRG_494t1:c.110C>T
  • LRG_494t2:c.11C>T
  • LRG_494:g.17175C>T
  • LRG_494p1:p.Ser37Leu
  • LRG_494p2:p.Ser4Leu
  • NC_000011.9:g.44129273C>T
Protein change:
S37L; SER4LEU
Links:
OMIM: 608210.0009; dbSNP: rs527624522
NCBI 1000 Genomes Browser:
rs527624522
Molecular consequence:
  • NM_000401.3:c.110C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001178083.2:c.11C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_207122.1:c.11C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Seizures, scoliosis, and macrocephaly syndrome (SSMS)
Synonyms:
SEIZURES, SCOLIOSIS, AND MACROCEPHALY/MICROCEPHALY SYNDROME
Identifiers:
MONDO: MONDO:0014731; MedGen: C4225248; OMIM: 616682

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000783102Marseille Medical Genetics, U1251,Aix Marseille University, Insermcriteria provided, single submitter
Likely pathogenic
(Jul 7, 2018)
inheritedresearch

SCV000930612OMIMno assertion criteria providedPathogenic
(Nov 6, 2020)
germlineliterature only

El-Bazzal, L., Atkinson, A., Gillart, A.-C., Obeid, M., Delague, V., Megarbane, A. A novel EXT2 mutation in a consanguineous family with severe developmental delay, microcephaly, seizures, feeding difficulties, and osteopenia extends the phenotypic spectrum of autosomal recessive EXT2-related syndrome (AREXT2). Europ. J. Med. Genet. 62: 259-264, 2019.

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
Syrianinheritedyes2not providednot providednot providednot providedresearch

Details of each submission

From Marseille Medical Genetics, U1251,Aix Marseille University, Inserm, SCV000783102.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1Syrian1not providednot providedresearchnot provided
2Syrian1not providednot providedresearchnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1inheritedyesnot providednot providednot provided1not providednot providednot provided
2inheritedyesnot providednot providednot provided1not providednot providednot provided

From OMIM, SCV000930612.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature onlynot provided

Description

In 2 brothers, born of consanguineous Syrian parents, with seizures, scoliosis, and microcephaly syndrome (SSMS; 616682), El-Bazzal et al. (2019) identified a homozygous c.11C-T transition (c.11C-T, NM_207122) in exon 2 of the EXT2 gene, resulting in a ser4-to-leu (S4L) substitution at a conserved residue. The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the family. It was found at a low frequency in the gnomAD database (6.908 x 10(-5)). Functional studies of the variant and studies of patient cells were not performed.

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

Last Updated: Aug 27, 2021

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