NM_014319.5(LEMD3):c.371G>A (p.Gly124Asp) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 1, 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:: RCV001945052.5

Allele description [Variation Report for NM_014319.5(LEMD3):c.371G>A (p.Gly124Asp)]

NM_014319.5(LEMD3):c.371G>A (p.Gly124Asp)

Genes:

LOC130008224:ATAC-STARR-seq lymphoblastoid silent region 4630 [Gene]
LEMD3:LEM domain containing 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

12q14.3

Genomic location:

Preferred name:

NM_014319.5(LEMD3):c.371G>A (p.Gly124Asp)

HGVS:

NC_000012.12:g.65169967G>A
NG_016210.2:g.5397G>A
NM_001167614.2:c.371G>A
NM_014319.5:c.371G>AMANE SELECT
NP_001161086.1:p.Gly124Asp
NP_055134.2:p.Gly124Asp
NC_000012.11:g.65563747G>A

Protein change:

G124D

Links:

dbSNP: rs892832101

NCBI 1000 Genomes Browser:

rs892832101

Molecular consequence:

NM_001167614.2:c.371G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_014319.5:c.371G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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cytochrome oxidase subunit II, partial (mitochondrion) [Brachycaudus amygdalinus...
cytochrome oxidase subunit II, partial (mitochondrion) [Brachycaudus amygdalinus]
gi|162289274|gb|ABX83490.1|

Protein
Zabrus vasconicus isolate indv1 cytochrome oxidase subunit I gene, partial cds; ...
Zabrus vasconicus isolate indv1 cytochrome oxidase subunit I gene, partial cds; and tRNA-Leu gene, partial sequence; mitochondrial
gi|46484894|gb|AY551904.1|

Nucleotide
FGGY carbohydrate kinase domain-containing protein isoform b [Homo sapiens]
FGGY carbohydrate kinase domain-containing protein isoform b [Homo sapiens]
gi|164663828|ref|NP_060761.3|

Protein
RecName: Full=UvrABC system protein C; Short=Protein UvrC; AltName: Full=Excinuc...
RecName: Full=UvrABC system protein C; Short=Protein UvrC; AltName: Full=Excinuclease ABC subunit C
gi|189038062|sp|A2RLW6.1|UVRC_LACLM

Protein
RecName: Full=Small ribosomal subunit protein bS18; AltName: Full=30S ribosomal ...
RecName: Full=Small ribosomal subunit protein bS18; AltName: Full=30S ribosomal protein S18
gi|166220956|sp|A2RNZ2.1|RS18_LACLM

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002180111	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 1, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002180111

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 1, 2023)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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, SCV002180111.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This sequence change replaces glycine, which is neutral and non-polar, with aspartic acid, which is acidic and polar, at codon 124 of the LEMD3 protein (p.Gly124Asp). This variant is present in population databases (no rsID available, gnomAD 0.04%). This variant has not been reported in the literature in individuals affected with LEMD3-related conditions. ClinVar contains an entry for this variant (Variation ID: 1413544). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant¬†is likely to be tolerated. 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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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