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NM_006306.4(SMC1A):c.1756C>T (p.Arg586Trp) AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jul 25, 2022
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV003107943.3

Allele description [Variation Report for NM_006306.4(SMC1A):c.1756C>T (p.Arg586Trp)]

NM_006306.4(SMC1A):c.1756C>T (p.Arg586Trp)

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.1756C>T (p.Arg586Trp)
HGVS:
  • NC_000023.11:g.53405648G>A
  • NG_006988.2:g.22023C>T
  • NM_001281463.1:c.1690C>T
  • NM_006306.4:c.1756C>TMANE SELECT
  • NP_001268392.1:p.Arg564Trp
  • NP_006297.2:p.Arg586Trp
  • LRG_773t1:c.1690C>T
  • LRG_773:g.22023C>T
  • LRG_773p1:p.Arg564Trp
  • NC_000023.10:g.53432580G>A
  • NM_006306.2:c.1756C>T
Protein change:
R564W
Links:
dbSNP: rs2146599836
NCBI 1000 Genomes Browser:
rs2146599836
Molecular consequence:
  • NM_001281463.1:c.1690C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006306.4:c.1756C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003761910GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)		Likely pathogenic
(Jul 25, 2022) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From GeneDx, SCV003761910.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Observed in a patient in the published literature, but additional clinical information was not included (Huisman et al., 2017); Missense variants in this gene are often considered pathogenic (HGMD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 28548707, 33502061)

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

Last Updated: Dec 24, 2023