NM_001034850.2(RETREG1):c.86C>T (p.Pro29Leu) AND not provided

Clinical significance:Conflicting interpretations of pathogenicity, Likely benign(2);Uncertain significance(1) (Last evaluated: Jan 6, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000756131.5

Allele description [Variation Report for NM_001034850.2(RETREG1):c.86C>T (p.Pro29Leu)]

NM_001034850.2(RETREG1):c.86C>T (p.Pro29Leu)

Genes:
RETREG1-AS1:RETREG1 antisense RNA 1 [Gene - HGNC]
RETREG1:reticulophagy regulator 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
5p15.1
Genomic location:
Preferred name:
NM_001034850.2(RETREG1):c.86C>T (p.Pro29Leu)
HGVS:
  • NC_000005.10:g.16616886G>A
  • NG_016644.2:g.5124C>T
  • NM_001034850.2:c.86C>T
  • NP_001030022.1:p.Pro29Leu
  • LRG_363t1:c.86C>T
  • LRG_363:g.5124C>T
  • LRG_363p1:p.Pro29Leu
  • NC_000005.9:g.16616995G>A
Protein change:
P29L
Links:
dbSNP: rs528532732
NCBI 1000 Genomes Browser:
rs528532732
Molecular consequence:
  • NM_001034850.2:c.86C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000769093Invitaecriteria provided, single submitter
Likely benign
(Aug 5, 2019)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV000883850ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratoriescriteria provided, single submitter
Uncertain significance
(Apr 25, 2018)
germlineclinical testing

Citation Link,

SCV001794101GeneDxcriteria provided, single submitter
Likely benign
(Jan 6, 2020)
germlineclinical testing

Citation Link

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000769093.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories, SCV000883850.1

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

Description

The FAM134B (aka RETREG1) c.86C>T; p.Pro29Leu variant (rs528532732), to our knowledge, is not reported in the medical literature, gene specific variation databases, nor has it been previously identified by our laboratory. This variant is listed in the genome Aggregation Database (gnomAD) with an East Asian population frequency of 0.3% (identified on 15 out of 5840 chromosomes). The proline at position 29 is weakly conserved, considering 11 species, and computational analyses of the effects of the p.Pro29Leu variant on protein structure and function do not predict a deleterious effect (SIFT: tolerated, PolyPhen-2: benign). Based on the available information, the clinical significance of the p.Pro29Leu variant cannot be determined with certainty.

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

From GeneDx, SCV001794101.1

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

Description

Has not been previously published as pathogenic or benign to our knowledge

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

Last Updated: Sep 24, 2021

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