NM_000401.3(EXT2):c.2015C>T (p.Thr672Met) AND Seizures, scoliosis, and macrocephaly syndrome

Clinical significance:Uncertain significance (Last evaluated: Jul 24, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000660594.2

Allele description [Variation Report for NM_000401.3(EXT2):c.2015C>T (p.Thr672Met)]

NM_000401.3(EXT2):c.2015C>T (p.Thr672Met)

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.2015C>T (p.Thr672Met)
Other names:
EXT2, THR672MET (rs138722406)
HGVS:
  • NC_000011.10:g.44234224C>T
  • NG_007560.1:g.143676C>T
  • NM_000401.3:c.2015C>T
  • NM_001178083.2:c.1946C>T
  • NM_207122.1:c.1916C>T
  • NP_000392.3:p.Thr672Met
  • NP_001171554.1:p.Thr649Met
  • NP_997005.1:p.Thr639Met
  • LRG_494t1:c.2015C>T
  • LRG_494t2:c.1916C>T
  • LRG_494:g.143676C>T
  • LRG_494p1:p.Thr672Met
  • LRG_494p2:p.Thr639Met
  • NC_000011.9:g.44255774C>T
Protein change:
T639M; THR672MET
Links:
OMIM: 608210.0011; dbSNP: rs138722406
NCBI 1000 Genomes Browser:
rs138722406
Molecular consequence:
  • NM_000401.3:c.2015C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001178083.2:c.1946C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_207122.1:c.1916C>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
SCV000782708Mayo Clinic Laboratories, Mayo Cliniccriteria provided, single submitter
Uncertain significance
(Jul 24, 2017)
maternalclinical testing

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

SCV000930614OMIMno assertion criteria providedPathogenic
(Aug 2, 2019)
germlineliterature only

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedmaternalunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

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]
PMID:
25741868
PMCID:
PMC4544753

Developmental delay, coarse facial features, and epilepsy in a patient with EXT2 gene variants.

Gupta A, Ewing SA, Renaud DL, Hasadsri L, Raymond KM, Klee EW, Gavrilova RH.

Clin Case Rep. 2019 Apr;7(4):632-637. doi: 10.1002/ccr3.2010.

PubMed [citation]
PMID:
30997052
PMCID:
PMC6452521

Details of each submission

From Mayo Clinic Laboratories, Mayo Clinic, SCV000782708.1

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

From OMIM, SCV000930614.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)

Description

For discussion of the c.2015C-T transition (.2015C-T, NM_000401.3) in exon 12 of the EXT2 gene, resulting in a thr672-to-met (T672M) substitution, that was found in compound heterozygous state in a patient with seizures, scoliosis, and macrocephaly syndrome (SSMS; 616682) by Gupta et al. (2019), see 608210.0010.

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

Last Updated: Aug 27, 2021

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