NM_001281463.1(SMC1A):c.793_795del (p.Lys265del) AND Congenital muscular hypertrophy-cerebral syndrome

Clinical significance:Uncertain significance (Last evaluated: Nov 3, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000639415.1

Allele description [Variation Report for NM_001281463.1(SMC1A):c.793_795del (p.Lys265del)]

NM_001281463.1(SMC1A):c.793_795del (p.Lys265del)

Gene:
SMC1A:structural maintenance of chromosomes 1A [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
Xp11.22
Genomic location:
Preferred name:
NM_001281463.1(SMC1A):c.793_795del (p.Lys265del)
HGVS:
  • NC_000023.11:g.53412249_53412251del
  • NG_006988.2:g.15422_15424del
  • NM_001281463.1:c.793_795del
  • NM_006306.3:c.859_861del
  • NP_001268392.1:p.Lys265del
  • NP_006297.2:p.Lys287del
  • LRG_773t1:c.793_795del
  • LRG_773t2:c.859_861del
  • LRG_773:g.15422_15424del
  • LRG_773p1:p.Lys265del
  • LRG_773p2:p.Lys287del
  • NC_000023.10:g.53439199_53439201del
  • NM_006306.3:c.859_861delAAG
Protein change:
K265del
Links:
dbSNP: rs1556890626
NCBI 1000 Genomes Browser:
rs1556890626
Molecular consequence:
  • NM_001281463.1:c.793_795del - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_006306.3:c.859_861del - inframe_deletion - [Sequence Ontology: SO:0001822]

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
SCV000760989Invitaecriteria provided, single submitter
Uncertain significance
(Nov 3, 2017)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000760989.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This variant, c.859_861delAAG, results in the deletion of 1 amino acids of the SMC1A protein (p.Lys287del), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with SMC1A-related disease. Experimental studies and prediction algorithms are not available for this variant, and the functional significance of the deleted amino acid is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Oct 7, 2021

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