NM_001084.5(PLOD3):c.668A>G (p.Asn223Ser) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 26, 2022
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:: RCV002512862.2

Allele description [Variation Report for NM_001084.5(PLOD3):c.668A>G (p.Asn223Ser)]

NM_001084.5(PLOD3):c.668A>G (p.Asn223Ser)

Gene:

PLOD3:procollagen-lysine,2-oxoglutarate 5-dioxygenase 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7q22.1

Genomic location:

Preferred name:

NM_001084.5(PLOD3):c.668A>G (p.Asn223Ser)

HGVS:

NC_000007.14:g.101215100T>C
NG_012148.1:g.7631A>G
NM_001084.5:c.668A>GMANE SELECT
NP_001075.1:p.Asn223Ser
NC_000007.13:g.100858381T>C
O60568:p.Asn223Ser

Protein change:

N223S; ASN223SER

Links:

UniProtKB: O60568#VAR_054913; OMIM: 603066.0001; dbSNP: rs121434414

NCBI 1000 Genomes Browser:

rs121434414

Molecular consequence:

NM_001084.5:c.668A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003440616	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 26, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 18834968, 30089812, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003440616

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 26, 2022)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

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

A connective tissue disorder caused by mutations of the lysyl hydroxylase 3 gene.

Salo AM, Cox H, Farndon P, Moss C, Grindulis H, Risteli M, Robins SP, Myllylä R.

Am J Hum Genet. 2008 Oct;83(4):495-503. doi: 10.1016/j.ajhg.2008.09.004. Epub 2008 Oct 2.

PubMed [citation]

PMID:: 18834968
PMCID:: PMC2561927

Molecular architecture of the multifunctional collagen lysyl hydroxylase and glycosyltransferase LH3.

Scietti L, Chiapparino A, De Giorgi F, Fumagalli M, Khoriauli L, Nergadze S, Basu S, Olieric V, Cucca L, Banushi B, Profumo A, Giulotto E, Gissen P, Forneris F.

Nat Commun. 2018 Aug 8;9(1):3163. doi: 10.1038/s41467-018-05631-5. Erratum in: Nat Commun. 2018 Sep 20;9(1):3912. doi: 10.1038/s41467-018-06481-x.

PubMed [citation]

PMID:: 30089812
PMCID:: PMC6082870

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003440616.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change replaces asparagine, which is neutral and polar, with serine, which is neutral and polar, at codon 223 of the PLOD3 protein (p.Asn223Ser). This variant is present in population databases (rs121434414, gnomAD 0.002%). This missense change has been observed in individual(s) with PLOD3-related conditions (PMID: 18834968). ClinVar contains an entry for this variant (Variation ID: 6643). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). Experimental studies have shown that this missense change affects PLOD3 function (PMID: 18834968, 30089812). 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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