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NM_006306.4(SMC1A):c.796AAG[2] (p.Lys268del) AND Congenital muscular hypertrophy-cerebral syndrome

Germline classification:
Pathogenic (4 submissions)
Last evaluated:
Jun 25, 2021
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000157049.10

Allele description [Variation Report for NM_006306.4(SMC1A):c.796AAG[2] (p.Lys268del)]

NM_006306.4(SMC1A):c.796AAG[2] (p.Lys268del)

Gene:
SMC1A:structural maintenance of chromosomes 1A [Gene - OMIM - HGNC]
Variant type:
Microsatellite
Cytogenetic location:
Xp11.22
Genomic location:
Preferred name:
NM_006306.4(SMC1A):c.796AAG[2] (p.Lys268del)
HGVS:
  • NC_000023.11:g.53412952TCT[2]
  • NG_006988.2:g.14713AAG[2]
  • NM_001281463.1:c.730AAG[2]
  • NM_006306.4:c.796AAG[2]MANE SELECT
  • NM_006306.4:c.802_804del
  • NP_001268392.1:p.Lys246del
  • NP_006297.2:p.Lys268del
  • LRG_773t1:c.730AAG[2]
  • LRG_773:g.14713AAG[2]
  • LRG_773p1:p.Lys246del
  • NC_000023.10:g.53439902TCT[2]
  • NM_006306.2:c.802_804del
  • NM_006306.3:c.802_804delAAG
  • NM_006306.4:c.802_804delMANE SELECT
  • NM_006306.4:c.802_804delAAGMANE SELECT
  • c.802_804del(p.K268del)
Protein change:
K246del
Links:
dbSNP: rs727503773
NCBI 1000 Genomes Browser:
rs727503773
Molecular consequence:
  • NM_001281463.1:c.730AAG[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_006306.4:c.796AAG[2] - inframe_deletion - [Sequence Ontology: SO:0001822]
Observations:
2

Condition(s)

Name:
Congenital muscular hypertrophy-cerebral syndrome (CDLS2)
Synonyms:
Cornelia de Lange syndrome 2
Identifiers:
MONDO: MONDO:0010370; MedGen: C1802395; Orphanet: 199; OMIM: 300590

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000195845Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine
no assertion criteria provided
Pathogenic
(Dec 2, 2014)
de novoresearch

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

SCV000248988Genetic Services Laboratory, University of Chicago
criteria provided, single submitter

(ACMG Guidelines, 2007)
Pathogenic
(Feb 8, 2013)
germlineclinical testing

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

SCV000747076Baylor Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jun 25, 2021)
unknownclinical testing

PubMed (2)
[See all records that cite these PMIDs]

SCV001712228Pediatric Genetics Clinic, Sheba Medical Center
no assertion criteria provided
Pathogenic
(May 13, 2021)
de novoclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedde novoyes2not providednot provided1not providedresearch, clinical testing

Citations

PubMed

Global transcriptional disturbances underlie Cornelia de Lange syndrome and related phenotypes.

Yuan B, Pehlivan D, Karaca E, Patel N, Charng WL, Gambin T, Gonzaga-Jauregui C, Sutton VR, Yesil G, Bozdogan ST, Tos T, Koparir A, Koparir E, Beck CR, Gu S, Aslan H, Yuregir OO, Al Rubeaan K, Alnaqeb D, Alshammari MJ, Bayram Y, Atik MM, et al.

J Clin Invest. 2015 Feb;125(2):636-51. doi: 10.1172/JCI77435. Epub 2015 Jan 9.

PubMed [citation]
PMID:
25574841
PMCID:
PMC4319410

ACMG recommendations for standards for interpretation and reporting of sequence variations: Revisions 2007.

Richards CS, Bale S, Bellissimo DB, Das S, Grody WW, Hegde MR, Lyon E, Ward BE; Molecular Subcommittee of the ACMG Laboratory Quality Assurance Committee..

Genet Med. 2008 Apr;10(4):294-300. doi: 10.1097/GIM.0b013e31816b5cae.

PubMed [citation]
PMID:
18414213
See all PubMed Citations (4)

Details of each submission

From Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine, SCV000195845.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedresearch PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1de novoyesnot providednot providednot provided1not providednot providednot provided

From Genetic Services Laboratory, University of Chicago, SCV000248988.1

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

From Baylor Genetics, SCV000747076.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Pediatric Genetics Clinic, Sheba Medical Center, SCV001712228.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1de novoyes1not providednot provided1not providednot providednot provided

Last Updated: Aug 13, 2023