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NM_001005373.4(LRSAM1):c.1993C>G (p.Pro665Ala) AND Charcot-Marie-Tooth disease axonal type 2P

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 8, 2019
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:
RCV001220288.8

Allele description [Variation Report for NM_001005373.4(LRSAM1):c.1993C>G (p.Pro665Ala)]

NM_001005373.4(LRSAM1):c.1993C>G (p.Pro665Ala)

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.1993C>G (p.Pro665Ala)
HGVS:
  • NC_000009.12:g.127501090C>G
  • NG_032008.1:g.54605C>G
  • NM_001005373.4:c.1993C>GMANE SELECT
  • NM_001005374.4:c.1993C>G
  • NM_001190723.3:c.1912C>G
  • NM_001384142.1:c.1993C>G
  • NM_001384143.1:c.1894C>G
  • NM_001384144.1:c.1204C>G
  • NM_138361.5:c.1993C>G
  • NP_001005373.1:p.Pro665Ala
  • NP_001005374.1:p.Pro665Ala
  • NP_001177652.1:p.Pro638Ala
  • NP_001371071.1:p.Pro665Ala
  • NP_001371072.1:p.Pro632Ala
  • NP_001371073.1:p.Pro402Ala
  • NP_612370.3:p.Pro665Ala
  • LRG_373t1:c.1993C>G
  • LRG_373:g.54605C>G
  • LRG_373p1:p.Pro665Ala
  • NC_000009.11:g.130263369C>G
  • NR_168891.1:n.2522C>G
  • NR_168892.1:n.2346C>G
Protein change:
P402A
Links:
dbSNP: rs749204843
NCBI 1000 Genomes Browser:
rs749204843
Molecular consequence:
  • NM_001005373.4:c.1993C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001005374.4:c.1993C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001190723.3:c.1912C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001384142.1:c.1993C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001384143.1:c.1894C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001384144.1:c.1204C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_138361.5:c.1993C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NR_168891.1:n.2522C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_168892.1:n.2346C>G - 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
SCV001392268Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(May 8, 2019) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001392268.5

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

Description

Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This variant has not been reported in the literature in individuals with LRSAM1-related conditions. This variant is present in population databases (rs749204843, ExAC 0.02%). This sequence change replaces proline with alanine at codon 665 of the LRSAM1 protein (p.Pro665Ala). The proline residue is moderately conserved and there is a small physicochemical difference between proline and alanine.

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

Last Updated: Sep 29, 2024