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NM_006306.4(SMC1A):c.1958C>T (p.Ser653Phe) AND Congenital muscular hypertrophy-cerebral syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jun 10, 2019
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:
RCV001270900.5

Allele description [Variation Report for NM_006306.4(SMC1A):c.1958C>T (p.Ser653Phe)]

NM_006306.4(SMC1A):c.1958C>T (p.Ser653Phe)

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.1958C>T (p.Ser653Phe)
HGVS:
  • NC_000023.11:g.53405345G>A
  • NG_006988.2:g.22326C>T
  • NM_001281463.1:c.1892C>T
  • NM_006306.4:c.1958C>TMANE SELECT
  • NP_001268392.1:p.Ser631Phe
  • NP_006297.2:p.Ser653Phe
  • LRG_773t1:c.1892C>T
  • LRG_773t2:c.1958C>T
  • LRG_773:g.22326C>T
  • LRG_773p1:p.Ser631Phe
  • NC_000023.10:g.53432277G>A
  • NM_006306.3:c.1958C>T
Protein change:
S631F
Links:
dbSNP: rs2075687166
NCBI 1000 Genomes Browser:
rs2075687166
Molecular consequence:
  • NM_001281463.1:c.1892C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006306.4:c.1958C>T - missense variant - [Sequence Ontology: SO:0001583]

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

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001451681Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSLVariantClassificationCriteria RUGD 01 April 2020)		Pathogenic
(Jun 10, 2019) 		unknownclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From Illumina Laboratory Services, Illumina, SCV001451681.1

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

Description

The SMC1A c.1958C>T (p.Ser653Phe) variant is a missense variant. A literature search was performed for the gene, cDNA change, and amino acid change. No publications were found based on this search. The p.Ser653Phe variant is not found in the Genome Aggregation Database in a region of good sequencing coverage, so the variant is presumed to be rare. Analyses by multiple in silico tools predict that the variant is deleterious. Based on the variant’s apparent de novo state, the presence of the variant in affected relatives, its rarity, and application of the ACMG criteria, the SMC1A p.Ser653Phe variant is classified as pathogenic for Cornelia de Lange syndrome.

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

Last Updated: Jun 23, 2024