NM_006306.4(SMC1A):c.793_795del (p.Glu265del) AND not provided

Clinical significance:Conflicting interpretations of pathogenicity, Pathogenic(1);Uncertain significance(1) (Last evaluated: Dec 24, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000999456.3

Allele description [Variation Report for NM_006306.4(SMC1A):c.793_795del (p.Glu265del)]

NM_006306.4(SMC1A):c.793_795del (p.Glu265del)

Gene:
SMC1A:structural maintenance of chromosomes 1A [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
Xp11.22
Genomic location:
Preferred name:
NM_006306.4(SMC1A):c.793_795del (p.Glu265del)
HGVS:
  • NC_000023.11:g.53412961_53412963del
  • NG_006988.2:g.14710_14712del
  • NM_001281463.1:c.727_729del
  • NM_006306.4:c.793_795delMANE SELECT
  • NP_001268392.1:p.Glu243del
  • NP_006297.2:p.Glu265del
  • LRG_773t1:c.727_729del
  • LRG_773:g.14710_14712del
  • LRG_773p1:p.Glu243del
  • NC_000023.10:g.53439911_53439913del
  • NM_006306.2:c.793_795delGAG
Protein change:
E243del
Links:
dbSNP: rs1602413408
NCBI 1000 Genomes Browser:
rs1602413408
Molecular consequence:
  • NM_001281463.1:c.727_729del - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_006306.4:c.793_795del - inframe_deletion - [Sequence Ontology: SO:0001822]
Observations:
1

Condition(s)

Identifiers:
MedGen: CN517202

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001156069CeGaT Praxis fuer Humangenetik Tuebingencriteria provided, single submitter
Uncertain significance
(Aug 1, 2018)
germlineclinical testing

Citation Link,

SCV001245515GeneDxcriteria provided, single submitter
Pathogenic
(Dec 24, 2019)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing

Details of each submission

From CeGaT Praxis fuer Humangenetik Tuebingen, SCV001156069.7

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

From GeneDx, SCV001245515.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providedclinical testingnot provided

Description

The c.793_795delGAG variant in the SMC1A gene has been observed in the mosaic state in GeneDx sequencing data in association with global developmental delay, short stature, microcephaly, and dysmorphic features. The c.793_795delGAG variant causes an in-frame deletion of one amino acid in a non-repeat region. In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect. The c.793_795delGAG variant is not observed in large population cohorts (Lek et al., 2016). Therefore, we interpret c.793_795delGAG as a pathogenic variant.

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

Last Updated: Oct 6, 2021

Support Center