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NM_001005373.4(LRSAM1):c.2011C>T (p.Gln671Ter) AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Nov 7, 2023
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:
RCV000214671.5

Allele description [Variation Report for NM_001005373.4(LRSAM1):c.2011C>T (p.Gln671Ter)]

NM_001005373.4(LRSAM1):c.2011C>T (p.Gln671Ter)

Gene:
LRSAM1:leucine rich repeat and sterile alpha motif containing 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
9q34.11
Genomic location:
Preferred name:
NM_001005373.4(LRSAM1):c.2011C>T (p.Gln671Ter)
HGVS:
  • NC_000009.12:g.127501108C>T
  • NG_032008.1:g.54623C>T
  • NM_001005373.4:c.2011C>TMANE SELECT
  • NM_001005374.4:c.2011C>T
  • NM_001190723.3:c.1930C>T
  • NM_001384142.1:c.2011C>T
  • NM_001384143.1:c.1912C>T
  • NM_001384144.1:c.1222C>T
  • NM_138361.5:c.2011C>T
  • NP_001005373.1:p.Gln671Ter
  • NP_001005374.1:p.Gln671Ter
  • NP_001005374.1:p.Gln671Ter
  • NP_001177652.1:p.Gln644Ter
  • NP_001371071.1:p.Gln671Ter
  • NP_001371072.1:p.Gln638Ter
  • NP_001371073.1:p.Gln408Ter
  • NP_612370.3:p.Gln671Ter
  • LRG_373t1:c.2011C>T
  • LRG_373:g.54623C>T
  • LRG_373p1:p.Gln671Ter
  • NC_000009.11:g.130263387C>T
  • NM_001005374.3:c.2011C>T
  • NR_168891.1:n.2540C>T
  • NR_168892.1:n.2364C>T
Protein change:
Q408*
Links:
dbSNP: rs876661247
NCBI 1000 Genomes Browser:
rs876661247
Molecular consequence:
  • NR_168891.1:n.2540C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_168892.1:n.2364C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001005373.4:c.2011C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001005374.4:c.2011C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001190723.3:c.1930C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001384142.1:c.2011C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001384143.1:c.1912C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001384144.1:c.1222C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_138361.5:c.2011C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000279884GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)		Likely pathogenic
(Nov 7, 2023) 		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, SCV000279884.12

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

Description

Nonsense variant predicted to result in protein truncation, as the last 53 amino acids are lost, and other loss-of-function variants have been reported downstream in HGMD; Not observed at significant frequency in large population cohorts (gnomAD); Reported in an individual with Charcot-Marie-Tooth disease in published literature (PMID: 33414056); This variant is associated with the following publications: (PMID: 22781092, 33414056)

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

Last Updated: Nov 25, 2023