NM_006306.4(SMC1A):c.3115C>T (p.Gln1039Ter) AND Developmental and epileptic encephalopathy, 85, with or without midline brain defects

Clinical significance:Pathogenic (Last evaluated: Dec 1, 2020)

Review status:(0/4) 0 stars out of maximum of 4 stars

no assertion criteria provided

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001072129.3

Allele description [Variation Report for NM_006306.4(SMC1A):c.3115C>T (p.Gln1039Ter)]

NM_006306.4(SMC1A):c.3115C>T (p.Gln1039Ter)

Gene:
SMC1A:structural maintenance of chromosomes 1A [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xp11.22
Genomic location:
Preferred name:
NM_006306.4(SMC1A):c.3115C>T (p.Gln1039Ter)
HGVS:
  • NC_000023.11:g.53383112G>A
  • NG_006988.2:g.44559C>T
  • NM_001281463.1:c.3049C>T
  • NM_006306.4:c.3115C>TMANE SELECT
  • NP_001268392.1:p.Gln1017Ter
  • NP_006297.2:p.Gln1039Ter
  • LRG_773t1:c.3049C>T
  • LRG_773:g.44559C>T
  • LRG_773p1:p.Gln1017Ter
  • NC_000023.10:g.53410033G>A
Protein change:
Q1017*; GLN1039TER
Links:
OMIM: 300040.0013
Molecular consequence:
  • NM_001281463.1:c.3049C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_006306.4:c.3115C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Developmental and epileptic encephalopathy, 85, with or without midline brain defects
Synonyms:
EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 85, WITH OR WITHOUT MIDLINE BRAIN DEFECTS
Identifiers:
MONDO: MONDO:0026771; MedGen: C5393312; OMIM: 301044

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001237472OMIMno assertion criteria providedPathogenic
(Dec 1, 2020)
germlineliterature only

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

Summary from all submissions

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

Citations

PubMed

Heterozygous truncation mutations of the SMC1A gene cause a severe early onset epilepsy with cluster seizures in females: Detailed phenotyping of 10 new cases.

Symonds JD, Joss S, Metcalfe KA, Somarathi S, Cruden J, Devlin AM, Donaldson A, DiDonato N, Fitzpatrick D, Kaiser FJ, Lampe AK, Lees MM, McLellan A, Montgomery T, Mundada V, Nairn L, Sarkar A, Schallner J, Pozojevic J, Parenti I, Tan J, Turnpenny P, et al.

Epilepsia. 2017 Apr;58(4):565-575. doi: 10.1111/epi.13669. Epub 2017 Feb 6.

PubMed [citation]
PMID:
28166369

Details of each submission

From OMIM, SCV001237472.2

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

Description

In a girl (patient 10) who died at age 9 years with developmental and epileptic encephalopathy-85 with abnormal corpus callosum (DEE85; 301044), Symonds et al. (2017) identified a de novo heterozygous c.3115C-T transition (c.3115C-T, NM_006306) in the SMC1A gene, predicted to result in a gln1039-to-ter (Q1039X) substitution. Functional studies of the variant and studies in patient cells were not performed, but X-inactivation studies showed a skewed ratio (76:24). The patient had onset of intractable tonic-clonic seizures at 2 months of age.

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

Last Updated: Sep 29, 2021

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