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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

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

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