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NM_002764.4(PRPS1):c.444G>A (p.Glu148=) AND Nephrolithiasis/nephrocalcinosis

Germline classification:
Likely benign (1 submission)
Last evaluated:
Jul 11, 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:
RCV004022121.1

Allele description [Variation Report for NM_002764.4(PRPS1):c.444G>A (p.Glu148=)]

NM_002764.4(PRPS1):c.444G>A (p.Glu148=)

Gene:
PRPS1:phosphoribosyl pyrophosphate synthetase 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xq22.3
Genomic location:
Preferred name:
NM_002764.4(PRPS1):c.444G>A (p.Glu148=)
HGVS:
  • NC_000023.11:g.107642404G>A
  • NG_008407.1:g.18981G>A
  • NM_001204402.2:c.-82-2773G>A
  • NM_002764.4:c.444G>AMANE SELECT
  • NP_002755.1:p.Glu148=
  • NP_002755.1:p.Glu148=
  • LRG_264t1:c.444G>A
  • LRG_264:g.18981G>A
  • LRG_264p1:p.Glu148=
  • NC_000023.10:g.106885634G>A
  • NM_002764.3:c.444G>A
Links:
dbSNP: rs201285459
NCBI 1000 Genomes Browser:
rs201285459
Molecular consequence:
  • NM_001204402.2:c.-82-2773G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_002764.4:c.444G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Nephrolithiasis/nephrocalcinosis
Identifiers:
MedGen: CN580796

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002637126Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely benign
(Jul 11, 2019) 		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 Ambry Genetics, SCV002637126.2

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

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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

Last Updated: Nov 10, 2024