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NM_017654.4(SAMD9):c.2053C>T (p.Arg685Ter) AND MIRAGE syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 17, 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:
RCV002291750.1

Allele description [Variation Report for NM_017654.4(SAMD9):c.2053C>T (p.Arg685Ter)]

NM_017654.4(SAMD9):c.2053C>T (p.Arg685Ter)

Gene:
SAMD9:sterile alpha motif domain containing 9 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7q21.2
Genomic location:
Preferred name:
NM_017654.4(SAMD9):c.2053C>T (p.Arg685Ter)
HGVS:
  • NC_000007.14:g.93104045G>A
  • NG_023419.1:g.18979C>T
  • NM_001193307.2:c.2053C>T
  • NM_017654.4:c.2053C>TMANE SELECT
  • NP_001180236.1:p.Arg685Ter
  • NP_060124.2:p.Arg685Ter
  • NC_000007.13:g.92733358G>A
  • NM_017654.3:c.2053C>T
Protein change:
R685*
Links:
dbSNP: rs763070754
NCBI 1000 Genomes Browser:
rs763070754
Molecular consequence:
  • NM_001193307.2:c.2053C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_017654.4:c.2053C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
MIRAGE syndrome
Synonyms:
MYELODYSPLASIA, INFECTION, RESTRICTION OF GROWTH, ADRENAL HYPOPLASIA, GENITAL PHENOTYPES, AND ENTEROPATHY
Identifiers:
MONDO: MONDO:0014888; MedGen: C4284088; OMIM: 617053

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002584561St. Jude Molecular Pathology, St. Jude Children's Research Hospital
criteria provided, single submitter

(St. Jude Assertion Criteria 2020)		Uncertain significance
(Aug 17, 2022) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From St. Jude Molecular Pathology, St. Jude Children's Research Hospital, SCV002584561.1

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

Description

The SAMD9 c.2053C>T (p.Arg685Ter) change is a nonsense variant that is predicted to cause premature protein truncation, however the functional significance of this variant is currently unknown. This variant has a maximum subpopulation frequency of 0.026% in gnomAD v2.1.1 (https://gnomad.broadinstitute.org/). This variant was identified as somatic in a patient with MIRAGE syndrome and no hematological features who harbored a germline SAMD9 p.Ala722Glu variant. These variants were determined to be on the same allele, and the p.Arg685Ter functioned as a second-site reversion mutation to undo the cellular growth repression caused by the germline SAMD9 variant. In summary, the evidence currently available is insufficient to determine the clinical significance of this variant. It has therefore been classified as of uncertain significance.

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

Last Updated: Oct 13, 2024