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NM_001005373.4(LRSAM1):c.2019dup (p.Glu674fs) AND Charcot-Marie-Tooth disease axonal type 2P

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Nov 24, 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:
RCV000806958.7

Allele description [Variation Report for NM_001005373.4(LRSAM1):c.2019dup (p.Glu674fs)]

NM_001005373.4(LRSAM1):c.2019dup (p.Glu674fs)

Gene:
LRSAM1:leucine rich repeat and sterile alpha motif containing 1 [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
9q34.11
Genomic location:
Preferred name:
NM_001005373.4(LRSAM1):c.2019dup (p.Glu674fs)
Other names:
p.Glu674Argfs*83
HGVS:
  • NC_000009.12:g.127501116dup
  • NG_032008.1:g.54631dup
  • NM_001005373.4:c.2019dupMANE SELECT
  • NM_001005374.4:c.2019dup
  • NM_001190723.3:c.1938dup
  • NM_001384142.1:c.2019dup
  • NM_001384143.1:c.1920dup
  • NM_001384144.1:c.1230dup
  • NM_138361.5:c.2019dup
  • NP_001005373.1:p.Glu674fs
  • NP_001005374.1:p.Glu674fs
  • NP_001177652.1:p.Glu647fs
  • NP_001371071.1:p.Glu674fs
  • NP_001371072.1:p.Glu641fs
  • NP_001371073.1:p.Glu411fs
  • NP_612370.3:p.Glu674fs
  • LRG_373t1:c.2019dup
  • LRG_373:g.54631dup
  • LRG_373p1:p.Glu674fs
  • NC_000009.11:g.130263394_130263395insA
  • NC_000009.11:g.130263395dup
  • NM_138361.4:c.2019dupA
  • NM_138361.5:c.2019dupA
  • NR_168891.1:n.2548dup
  • NR_168892.1:n.2372dup
Protein change:
E411fs
Links:
dbSNP: rs1315010600
NCBI 1000 Genomes Browser:
rs1315010600
Molecular consequence:
  • NM_001005373.4:c.2019dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001005374.4:c.2019dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001190723.3:c.1938dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001384142.1:c.2019dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001384143.1:c.1920dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001384144.1:c.1230dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_138361.5:c.2019dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NR_168891.1:n.2548dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_168892.1:n.2372dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Charcot-Marie-Tooth disease axonal type 2P
Synonyms:
CHARCOT-MARIE-TOOTH NEUROPATHY, TYPE 2P; Charcot-Marie-Tooth disease type 2P; CHARCOT-MARIE-TOOTH DISEASE, AXONAL, TYPE 2G; See all synonyms [MedGen]
Identifiers:
Gene: 431712; MONDO: MONDO:0013753; MedGen: C3280797; Orphanet: 300319; Orphanet: 99941; OMIM: 614436

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000946982Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Nov 24, 2023) 		germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Diagnostic utility of exome sequencing in the evaluation of neuromuscular disorders.

Haskell GT, Adams MC, Fan Z, Amin K, Guzman Badillo RJ, Zhou L, Bizon C, Chahin N, Greenwood RS, Milko LV, Shiloh-Malawsky Y, Crooks KR, Strande N, Tennison M, Tilley CR, Brandt A, Wilhelmsen KC, Weck K, Evans JP, Berg JS.

Neurol Genet. 2018 Feb;4(1):e212. doi: 10.1212/NXG.0000000000000212.

PubMed [citation]
PMID:
29417091
PMCID:
PMC5798313

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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000946982.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

This sequence change creates a premature translational stop signal (p.Glu674Argfs*83) in the LRSAM1 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 50 amino acid(s) of the LRSAM1 protein. This variant is present in population databases (no rsID available, gnomAD 0.0009%). This premature translational stop signal has been observed in individual(s) with clinical features of autosomal recessive neuropathy (PMID: 29417091; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 651567). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Sep 29, 2024