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NM_000302.4(PLOD1):c.1533C>G (p.Tyr511Ter) AND PLOD1-related condition

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Nov 15, 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:
RCV003904842.1

Allele description [Variation Report for NM_000302.4(PLOD1):c.1533C>G (p.Tyr511Ter)]

NM_000302.4(PLOD1):c.1533C>G (p.Tyr511Ter)

Gene:
PLOD1:procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p36.22
Genomic location:
Preferred name:
NM_000302.4(PLOD1):c.1533C>G (p.Tyr511Ter)
Other names:
p.Tyr511*
HGVS:
  • NC_000001.11:g.11965542C>G
  • NG_008159.1:g.35854C>G
  • NM_000302.4:c.1533C>GMANE SELECT
  • NM_001316320.2:c.1674C>G
  • NP_000293.2:p.Tyr511Ter
  • NP_001303249.1:p.Tyr558Ter
  • NC_000001.10:g.12025599C>G
  • NM_000302.3:c.1533C>G
Protein change:
Y511*; TYR511TER
Links:
OMIM: 153454.0007; dbSNP: rs121913552
NCBI 1000 Genomes Browser:
rs121913552
Molecular consequence:
  • NM_000302.4:c.1533C>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001316320.2:c.1674C>G - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
PLOD1-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004719212PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Nov 15, 2023) 		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

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004719212.1

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

Description

The PLOD1 c.1533C>G variant is predicted to result in premature protein termination (p.Tyr511*). This variant was reported, along with another pathogenic variant, in an individual with Ehlers-Danlos syndrome VI (Yeowell et al. 1997. PubMed ID: 9220536). This variant is reported in 0.0040% of alleles in individuals of African descent in gnomAD (http://gnomad.broadinstitute.org/variant/1-12025599-C-G). Nonsense variants in PLOD1 are expected to be pathogenic. This variant is interpreted as pathogenic.

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

Last Updated: May 1, 2024