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NM_001177316.2(SLC34A3):c.-40+71G>A AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jun 15, 2016
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:
RCV000586817.2

Allele description [Variation Report for NM_001177316.2(SLC34A3):c.-40+71G>A]

NM_001177316.2(SLC34A3):c.-40+71G>A

Gene:
SLC34A3:solute carrier family 34 member 3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
9q34.3
Genomic location:
Preferred name:
NM_001177316.2(SLC34A3):c.-40+71G>A
HGVS:
  • NC_000009.12:g.137231009G>A
  • NG_017008.2:g.5109G>A
  • NM_001177316.2:c.-40+71G>AMANE SELECT
  • NM_001177317.2:c.-43+71G>A
  • NM_080877.3:c.-110G>A
  • NC_000009.11:g.140125461G>A
  • NM_080877.2:c.-110G>A
Links:
dbSNP: rs1554782358
NCBI 1000 Genomes Browser:
rs1554782358
Molecular consequence:
  • NM_080877.3:c.-110G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001177316.2:c.-40+71G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001177317.2:c.-43+71G>A - 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
SCV000699831Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Uncertain significance
(Jun 15, 2016) 		germlineclinical testing

LabCorp Variant Classification Summary - May 2015.docx

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 Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000699831.1

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

Description

Variant summary: SLC34A3c.-110G>A is located at a non-conserved nucleotide in the 5UTR of the SLC34A3 gene. One in silico tool predicts a benign outcome, and 4/5 splicing algorithms predict no significant change to splicing. Mutations in this gene are associated with hereditary hypophosphatemic rickets with hypercalciuria, and alternatively spliced transcript variants varying in the 5' UTR have been found for this gene. However, this particular 5 UTR variant has not been cited in the literature, publically available databases, or classified by other clinical labs. The frequency in large general population cohorts (i.e. ExAC) cannot be determined since coverage is insufficient at this genomic location. Taken together, this variant was classified as a VUS until additional information is available.

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

Last Updated: May 24, 2022