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NM_001128225.3(SLC39A13):c.-9+3G>T AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 30, 2017
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:
RCV000498709.1

Allele description [Variation Report for NM_001128225.3(SLC39A13):c.-9+3G>T]

NM_001128225.3(SLC39A13):c.-9+3G>T

Genes:
SLC39A13-AS1:SLC39A13 antisense RNA 1 [Gene - HGNC]
SLC39A13:solute carrier family 39 member 13 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11p11.2
Genomic location:
Preferred name:
NM_001128225.3(SLC39A13):c.-9+3G>T
HGVS:
  • NC_000011.10:g.47408665G>T
  • NG_017073.1:g.5171G>T
  • NM_001128225.3:c.-9+3G>TMANE SELECT
  • NM_001330245.2:c.-9+3G>T
  • NM_152264.5:c.-30+3G>T
  • NC_000011.9:g.47430216G>T
  • NM_152264.4:c.-30+3G>T
Links:
dbSNP: rs920033870
NCBI 1000 Genomes Browser:
rs920033870
Molecular consequence:
  • NM_001128225.3:c.-9+3G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001330245.2:c.-9+3G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_152264.5:c.-30+3G>T - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000590146GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(May 30, 2017) 		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, SCV000590146.3

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

Description

The c.-30+3 G>T variant of uncertain significance in the SLC39A13 gene has not been published as pathogenic or been reported as benign to our knowledge. This variant is located in intron 1 of the 5' untranslated region of the SLC39A13 gene, which is the non-coding region upstream of the start codon located in exon 2. Specifically, this variant occurs in the natural splice donor site of intron 1, at a nucleotide that is conserved in mammals. However, in silico splice algorithms predict that this variant likely does not alter splicing. Additionally, no other regulatory or splice site variants in the SLC39A13 gene have been reported in HGMD in association with spEDS to date (Stenson et al., 2014). Nevertheless, in the absence of functional mRNA studies, the physiological consequence of this variant cannot be precisely determined. Furthermore, data from control individuals was not available to assess whether c.-30+3 G>T may be a common benign variant in the general population.Therefore, based on the currently available information, it is unclear whether this variant is pathogenic or rare benign.

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

Last Updated: Mar 26, 2023