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NM_017654.4(SAMD9):c.2254T>A (p.Trp752Arg) AND Monosomy 7 myelodysplasia and leukemia syndrome 2

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Apr 3, 2023
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:
RCV003230288.1

Allele description [Variation Report for NM_017654.4(SAMD9):c.2254T>A (p.Trp752Arg)]

NM_017654.4(SAMD9):c.2254T>A (p.Trp752Arg)

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.2254T>A (p.Trp752Arg)
HGVS:
  • NC_000007.14:g.93103844A>T
  • NG_023419.1:g.19180T>A
  • NM_001193307.2:c.2254T>A
  • NM_017654.4:c.2254T>AMANE SELECT
  • NP_001180236.1:p.Trp752Arg
  • NP_060124.2:p.Trp752Arg
  • NC_000007.13:g.92733157A>T
  • NM_017654.3:c.2254T>A
Protein change:
W752R
Links:
dbSNP: rs148339415
NCBI 1000 Genomes Browser:
rs148339415
Molecular consequence:
  • NM_001193307.2:c.2254T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_017654.4:c.2254T>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Monosomy 7 myelodysplasia and leukemia syndrome 2
Identifiers:
MONDO: MONDO:0030801; MedGen: C5436668; OMIM: 619041

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003928095St. Jude Molecular Pathology, St. Jude Children's Research Hospital
criteria provided, single submitter

(St. Jude Assertion Criteria 2020)		Uncertain significance
(Apr 3, 2023) 		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, SCV003928095.1

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

Description

The SAMD9 c.2254T>A (p.Trp752Arg) missense change has a maximum subpopulation frequency of 0.017% in gnomAD v2.1.1 (https://gnomad.broadinstitute.org/). The in silico tool REVEL predicts a deleterious effect on protein function, however in silico predictions have not been found to correlate with syndromic risk and are thus not considered supporting evidence of a pathogenic or benign effect (PMID: 34621053). To our knowledge, this variant has not been reported in individuals with SAMD9-associated conditions. 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: Sep 29, 2024