NM_001005373.4(LRSAM1):c.268G>A (p.Asp90Asn) AND not provided

Clinical significance:Conflicting interpretations of pathogenicity, Benign(1);Uncertain significance(1) (Last evaluated: Apr 5, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
4 submissions [Details]
Record status:
current
Accession:
RCV000416142.6

Allele description [Variation Report for NM_001005373.4(LRSAM1):c.268G>A (p.Asp90Asn)]

NM_001005373.4(LRSAM1):c.268G>A (p.Asp90Asn)

Gene:
LRSAM1:leucine rich repeat and sterile alpha motif containing 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
9q33.3
Genomic location:
Preferred name:
NM_001005373.4(LRSAM1):c.268G>A (p.Asp90Asn)
HGVS:
  • NC_000009.12:g.127459018G>A
  • NG_032008.1:g.12533G>A
  • NM_001005373.4:c.268G>AMANE SELECT
  • NM_001005374.4:c.268G>A
  • NM_001190723.3:c.268G>A
  • NM_001384142.1:c.268G>A
  • NM_001384143.1:c.268G>A
  • NM_001384144.1:c.-517G>A
  • NM_138361.5:c.268G>A
  • NP_001005373.1:p.Asp90Asn
  • NP_001005374.1:p.Asp90Asn
  • NP_001177652.1:p.Asp90Asn
  • NP_001371071.1:p.Asp90Asn
  • NP_001371072.1:p.Asp90Asn
  • NP_612370.3:p.Asp90Asn
  • LRG_373t1:c.268G>A
  • LRG_373:g.12533G>A
  • LRG_373p1:p.Asp90Asn
  • NC_000009.11:g.130221297G>A
  • NR_168891.1:n.616G>A
  • NR_168892.1:n.616G>A
Protein change:
D90N
Links:
dbSNP: rs117692127
NCBI 1000 Genomes Browser:
rs117692127
Molecular consequence:
  • NM_001384144.1:c.-517G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001005373.4:c.268G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001005374.4:c.268G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001190723.3:c.268G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001384142.1:c.268G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001384143.1:c.268G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_138361.5:c.268G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_168891.1:n.616G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_168892.1:n.616G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
2

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000279018GeneDxcriteria provided, single submitter
Benign
(Apr 5, 2019)
germlineclinical testing

Citation Link,

SCV000493555CeGaT Praxis fuer Humangenetik Tuebingencriteria provided, single submitter
Uncertain significance
(Aug 1, 2017)
germlineclinical testing

Citation Link,

SCV001922728Clinical Genetics,Academic Medical Center - VKGL Data-share Consensus

See additional submitters

no assertion criteria providedLikely benigngermlineclinical testing

SCV001930124Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus

See additional submitters

no assertion criteria providedLikely benigngermlineclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes2not providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000279018.7

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

Description

This variant is associated with the following publications: (PMID: 32376792)

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

From CeGaT Praxis fuer Humangenetik Tuebingen, SCV000493555.13

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided2not providednot providednot provided

From Clinical Genetics,Academic Medical Center - VKGL Data-share Consensus, SCV001922728.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus, SCV001930124.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 27, 2021

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